Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007334.1 Hibiscus syriacus cultivar Beakdansim tig00019627_pilon, whole genome shotgun sequence
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: 88066
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:142 original size:23 final size:24
Alignment explanation
Indices: 107--171 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 24
97 ATTTAAAAAA
**
107 TTATAAACTAAATAA-T-TTTAAT
1 TTATAAAAAAAATAACTATTTAAT
129 TTATTAAAAAAAATAAACTAAATTTAAT
1 TTA-TAAAAAAAAT-AACT--ATTTAAT
157 TTATAAAAAAAATAA
1 TTATAAAAAAAATAA
172 ATAATTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
22 3 0.09
23 8 0.23
24 2 0.06
25 1 0.03
26 2 0.06
27 10 0.29
28 9 0.26
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (24 bp):
TTATAAAAAAAATAACTATTTAAT
Found at i:155 original size:28 final size:27
Alignment explanation
Indices: 115--188 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 27
105 AATTATAAAC
115 TAAATAATTTTAATTTATTAAAAAAAA
1 TAAATAATTTTAATTTATTAAAAAAAA
*
142 TAAACTAAATTTAATTTA-TAAAAAAAA
1 TAAA-TAATTTTAATTTATTAAAAAAAA
169 TAAATAATTTTAAATTTATT
1 TAAATAATTTT-AATTTATT
189 TATATAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 6 0.14
27 23 0.55
28 13 0.31
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATAATTTTAATTTATTAAAAAAAA
Found at i:391 original size:30 final size:30
Alignment explanation
Indices: 323--393 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
313 GAAATGAAAC
* * *
323 TTTCAAAAGTTTAGGGATCAAAGTGTAAAG
1 TTTCAAAAGTTTAGGAATAAAAGTATAAAG
*
353 TTAT-AAAAGTTTAGTAACTAAAAGTATAAA-
1 TT-TCAAAAGTTTAGGAA-TAAAAGTATAAAG
383 TTTCAAAAGTT
1 TTTCAAAAGTT
394 ATATTTGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.03
30 22 0.65
31 11 0.32
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (30 bp):
TTTCAAAAGTTTAGGAATAAAAGTATAAAG
Found at i:6624 original size:19 final size:19
Alignment explanation
Indices: 6582--6652 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
6572 TGACTTCTGT
* * *
6582 GTTGCGAATTTGGAAACCGT
1 GTTGCGAA-TTCGAAATCGA
6602 GTTGCGAATTCGAAATCGA
1 GTTGCGAATTCGAAATCGA
* *
6621 GTTGCAAATTCGAAATTGA
1 GTTGCGAATTCGAAATCGA
*
6640 ATTGCGAATTCGA
1 GTTGCGAATTCGA
6653 TGGTTATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 36 0.82
20 8 0.18
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (19 bp):
GTTGCGAATTCGAAATCGA
Found at i:7176 original size:13 final size:13
Alignment explanation
Indices: 7151--7186 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
7141 AGAAAAGATG
*
7151 AAGAAGAAAAAAA
1 AAGAAGAAGAAAA
*
7164 AATAAGAAGAAAA
1 AAGAAGAAGAAAA
7177 AAGAAGAAGA
1 AAGAAGAAGA
7187 GTTGACGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAGAAGAAGAAAA
Found at i:7186 original size:16 final size:16
Alignment explanation
Indices: 7143--7186 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
7133 AATGAAAAAG
*
7143 AAAAGATGAAGAAGAA
1 AAAAGAAGAAGAAGAA
* *
7159 AAAAAAATAAGAAGAA
1 AAAAGAAGAAGAAGAA
7175 AAAAGAAGAAGA
1 AAAAGAAGAAGA
7187 GTTGACGTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (16 bp):
AAAAGAAGAAGAAGAA
Found at i:7437 original size:26 final size:28
Alignment explanation
Indices: 7402--7455 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
7392 TTCTTGTCCC
7402 TTTTTTGTTT-G-GTTG-TTTTGGTTTT
1 TTTTTTGTTTAGTGTTGATTTTGGTTTT
7427 TTTTTTAGTTTAGGTGTTGATTTTGGTTT
1 TTTTTT-GTTTA-GTGTTGATTTTGGTTT
7456 GCTTGGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 6 0.25
26 4 0.17
28 1 0.04
29 4 0.17
30 9 0.38
ACGTcount: A:0.06, C:0.00, G:0.24, T:0.70
Consensus pattern (28 bp):
TTTTTTGTTTAGTGTTGATTTTGGTTTT
Found at i:9497 original size:7 final size:7
Alignment explanation
Indices: 9487--9547 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
9477 ACCTTAAATC
9487 CTAAACT
1 CTAAACT
9494 CTAAAC-
1 CTAAACT
9500 CATAAACT
1 C-TAAACT
*
9508 CTAAACC
1 CTAAACT
9515 CTAAACT
1 CTAAACT
*
9522 TTAAACAT
1 CTAAAC-T
9530 -TAAAC-
1 CTAAACT
9535 CATAAACT
1 C-TAAACT
9543 CTAAA
1 CTAAA
9548 AGTAAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
6 1 0.02
7 41 0.91
8 3 0.07
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAAACT
Found at i:9498 original size:14 final size:13
Alignment explanation
Indices: 9481--9527 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
9471 CGTAAAACCT
9481 TAAATCCTAAACTC
1 TAAA-CCTAAACTC
9495 TAAACCATAAACTC
1 TAAACC-TAAACTC
*
9509 TAAACCCTAAACTT
1 TAAA-CCTAAACTC
9523 TAAAC
1 TAAAC
9528 ATTAAACCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 25 0.83
15 2 0.07
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAACCTAAACTC
Found at i:9500 original size:21 final size:21
Alignment explanation
Indices: 9475--9541 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
9465 AATTATCGTA
*
9475 AAACCTTAAA-TCCTAAACTCT
1 AAACCTTAAACT-CTAAACCCT
*
9496 AAACCATAAACTCTAAACCCT
1 AAACCTTAAACTCTAAACCCT
* *
9517 AAACTTTAAACAT-TAAACCAT
1 AAACCTTAAAC-TCTAAACCCT
9538 AAAC
1 AAAC
9542 TCTAAAAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 37 0.95
22 2 0.05
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACCTTAAACTCTAAACCCT
Found at i:9547 original size:14 final size:14
Alignment explanation
Indices: 9488--9527 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
9478 CCTTAAATCC
9488 TAAACTCTAAACCA
1 TAAACTCTAAACCA
*
9502 TAAACTCTAAACCC
1 TAAACTCTAAACCA
*
9516 TAAACTTTAAAC
1 TAAACTCTAAAC
9528 ATTAAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACTCTAAACCA
Found at i:11925 original size:14 final size:14
Alignment explanation
Indices: 11902--11931 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11892 GGAAATATGA
*
11902 CCTCCGAGGATCCT
1 CCTCCAAGGATCCT
11916 CCTCCAAGGATCCT
1 CCTCCAAGGATCCT
11930 CC
1 CC
11932 AAAGACATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.47, G:0.17, T:0.20
Consensus pattern (14 bp):
CCTCCAAGGATCCT
Found at i:13922 original size:13 final size:13
Alignment explanation
Indices: 13904--13943 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
13894 CTTCGGCCAG
13904 GCTGCATGTACAT
1 GCTGCATGTACAT
13917 GCTGCATGTACAT
1 GCTGCATGTACAT
*
13930 GCTGCATGTGCAT
1 GCTGCATGTACAT
13943 G
1 G
13944 GATTGCAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.30
Consensus pattern (13 bp):
GCTGCATGTACAT
Found at i:16035 original size:17 final size:18
Alignment explanation
Indices: 15995--16034 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
15985 ATAATACATA
* *
15995 AAAAATAATTATTATTTT
1 AAAAATAATAATAATTTT
16013 AAAAATAATAATAATTTT
1 AAAAATAATAATAATTTT
16031 AAAA
1 AAAA
16035 TTTTTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATAATAATAATTTT
Found at i:26445 original size:21 final size:21
Alignment explanation
Indices: 26369--26450 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
26359 TTGAGAGAAA
* *
26369 CCTCTTCAACGATGACAGTGG
1 CCTCTTGAACGATGACAGGGG
* * **
26390 CCTCTTGAATGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** *
26411 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
26432 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
26451 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:26954 original size:20 final size:20
Alignment explanation
Indices: 26929--27000 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
26919 TGAAACTTAA
26929 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
26949 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
26969 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
26989 ATCGCAATGCGA
1 ATCGCAACGCGA
27001 TTTTTATTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:27056 original size:20 final size:20
Alignment explanation
Indices: 27028--27131 Score: 112
Period size: 20 Copynumber: 5.5 Consensus size: 20
27018 GATTCTTTCG
* **
27028 TTGCAATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
27048 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
27068 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
27082 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
27102 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
27122 TTGCGATAGT
1 TTGCGATAGT
27132 AAACTATTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
14 7 0.10
16 6 0.09
18 5 0.07
20 52 0.74
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:27077 original size:54 final size:54
Alignment explanation
Indices: 26990--27128 Score: 190
Period size: 54 Copynumber: 2.6 Consensus size: 54
26980 AATTTGACTA
* ** *
26990 TCGCAATGCGATTTTTA-TTTCGCATTGCGATTCTTTCGTTGCAATAGTCAAAT
1 TCGCATTGCGATAGTTATTTTCGCATTGCGATTCTCTCGTTGCAATAGTCAAAT
* **
27043 TCGCATTGCGATAGTTATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTTATTTTCGCATTGCGATTCTCTCGTTGCAATAGTCAAAT
* *
27097 TCGCGTTGCGATAGTCATTTTCGCATTGCGAT
1 TCGCATTGCGATAGTTATTTTCGCATTGCGAT
27129 AGTAAACTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 14 0.18
54 62 0.82
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (54 bp):
TCGCATTGCGATAGTTATTTTCGCATTGCGATTCTCTCGTTGCAATAGTCAAAT
Found at i:30127 original size:20 final size:20
Alignment explanation
Indices: 30069--30138 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
30059 GAAACTTTAA
* **
30069 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
30089 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
30109 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
30129 ATCGCAACGC
1 ATCGCAACGC
30139 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:30572 original size:22 final size:22
Alignment explanation
Indices: 30510--30575 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
30500 TGACCGTGAA
* *
30510 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
30532 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
30554 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
30576 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:30794 original size:20 final size:20
Alignment explanation
Indices: 30771--30823 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
30761 CGATAGTCAG
*
30771 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
30791 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
30811 ATTCGCATTGCGA
1 ATTCGCATTGCGA
30824 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:30844 original size:21 final size:21
Alignment explanation
Indices: 30820--30865 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
30810 TATTCGCATT
30820 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
30841 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
30862 GCGA
1 GCGA
30866 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:34624 original size:4 final size:4
Alignment explanation
Indices: 34615--34645 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
34605 CGAATTCCAG
34615 CATC CATC CATC CATC CATC CATC CATC CAT
1 CATC CATC CATC CATC CATC CATC CATC CAT
34646 ACATAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
CATC
Found at i:39033 original size:25 final size:24
Alignment explanation
Indices: 38995--39044 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 24
38985 AAAAATGAAC
38995 CTTTAAAAATAATAAATAATAAAA
1 CTTTAAAAATAATAAATAATAAAA
39019 CTTTAAAAAATAATAAATAATAAAA
1 CTTT-AAAAATAATAAATAATAAAA
39044 C
1 C
39045 ATATTCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
CTTTAAAAATAATAAATAATAAAA
Found at i:39524 original size:30 final size:32
Alignment explanation
Indices: 39454--39537 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
39444 TTAAAATTTT
39454 AGGTACTAAAATGAAACAAAAAGTTAACAGCA
1 AGGTACTAAAATGAAACAAAAAGTTAACAGCA
* * *
39486 ATGTACTAAAATGAAATAAAAAGTTAA-TG-A
1 AGGTACTAAAATGAAACAAAAAGTTAACAGCA
*
39516 CGGTACTAAAATGAAACAAAAA
1 AGGTACTAAAATGAAACAAAAA
39538 TCAAACGTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 20 0.43
31 1 0.02
32 25 0.54
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (32 bp):
AGGTACTAAAATGAAACAAAAAGTTAACAGCA
Found at i:49844 original size:18 final size:18
Alignment explanation
Indices: 49821--49867 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
49811 GACCGGTCAC
*
49821 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCATT
49839 AACCCGACCCGACCCATT
1 AACCCGACCCGACCCATT
*
49857 TACCCGACCCG
1 AACCCGACCCG
49868 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.23, C:0.51, G:0.15, T:0.11
Consensus pattern (18 bp):
AACCCGACCCGACCCATT
Found at i:49861 original size:13 final size:13
Alignment explanation
Indices: 49844--49877 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
49834 CCGTTAACCC
49844 GACCCGACCCATT
1 GACCCGACCCATT
* *
49857 TACCCGACCCGTT
1 GACCCGACCCATT
49870 GACCCGAC
1 GACCCGAC
49878 TCGACCCGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.21, C:0.47, G:0.18, T:0.15
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:49862 original size:31 final size:31
Alignment explanation
Indices: 49826--49906 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
49816 GTCACAACCC
*
49826 GACCCGACCCGTTAACCCGACCCGACCCATT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
* * *
49857 TACCCGACCCGTTGACCCGACTCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
*
49888 GACTCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
49907 TTGACCGTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.46, G:0.20, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCATT
Found at i:49882 original size:18 final size:18
Alignment explanation
Indices: 49861--49895 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49851 CCCATTTACC
49861 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
49879 CGACCCGTTGACTCGAC
1 CGACCCGTTGACCCGAC
49896 CCGTTGACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:49891 original size:13 final size:13
Alignment explanation
Indices: 49875--49903 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
49865 CCGTTGACCC
49875 GACTCGACCCGTT
1 GACTCGACCCGTT
49888 GACTCGACCCGTT
1 GACTCGACCCGTT
49901 GAC
1 GAC
49904 CCGTTGACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.38, G:0.24, T:0.21
Consensus pattern (13 bp):
GACTCGACCCGTT
Found at i:51227 original size:18 final size:18
Alignment explanation
Indices: 51201--51235 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51191 TCGAAATGAC
*
51201 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
51219 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
51236 CAGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:54884 original size:2 final size:2
Alignment explanation
Indices: 54877--54906 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54867 AGTCCACTTC
54877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54907 TTCTAGGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61416 original size:29 final size:29
Alignment explanation
Indices: 61374--61455 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
61364 AAACTAAATT
61374 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
61403 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
61432 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
61456 GTTAGGTGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:66186 original size:29 final size:29
Alignment explanation
Indices: 66141--66222 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
66131 AAACTAAATT
*
66141 GATGTCATTGCTCACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
66170 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
66199 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
66223 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:67941 original size:21 final size:21
Alignment explanation
Indices: 67899--67941 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
67889 TTTCTGGGCT
* *
67899 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
67920 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
67941 A
1 A
67942 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:68871 original size:4 final size:4
Alignment explanation
Indices: 68862--69946 Score: 2105
Period size: 4 Copynumber: 273.2 Consensus size: 4
68852 AAATGATGAC
68862 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
68910 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
68958 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69006 ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69052 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69100 ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69146 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69194 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69242 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69290 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69338 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69386 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69434 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69482 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69530 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69578 ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69624 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69672 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69720 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69768 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69816 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
69862 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
69910 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
69947 AGGGTTATAT
Statistics
Matches: 1071, Mismatches: 2, Indels: 16
0.98 0.00 0.01
Matches are distributed among these distances:
2 8 0.01
4 1063 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:70159 original size:31 final size:31
Alignment explanation
Indices: 70121--70194 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
70111 GTCAAAGAAC
**
70121 TACCTATG-TCTTTCGAGACATATGGATAGTA
1 TACCTATGTTCTAACGA-ACATATGGATAGTA
* *
70152 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTAACGAACATATGGATAGTA
*
70183 TACCTAGGTTCT
1 TACCTATGTTCT
70195 TCGGTACCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGATAGTA
Found at i:70244 original size:30 final size:30
Alignment explanation
Indices: 70200--70361 Score: 279
Period size: 30 Copynumber: 5.4 Consensus size: 30
70190 GTTCTTCGGT
* *
70200 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
70230 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
*
70260 ACCTCTGGATAGTTACCGAAGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
70290 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
* *
70320 ACCTTTGGATAGTTACCGAAGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
70350 ACCTCTGGATAG
1 ACCTCTGGATAG
70362 GTCCTTCGGA
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 125 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:71042 original size:35 final size:35
Alignment explanation
Indices: 71002--71110 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
70992 CAATTATATA
*
71002 TATATATATAATGTTTTATATTTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTTATATTAAT
*
71037 TATATATATAATATTTT-TTTATTTTTTATATTAAT
1 TATATATATAATATTTTATAT-TTTTTTATATTAAT
71072 TATATATATAATATTTTATA--TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTTATATTAAT
71105 TATATA
1 TATATA
71111 ATACAAACCC
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
33 19 0.28
34 2 0.03
35 47 0.68
36 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (35 bp):
TATATATATAATATTTTATATTTTTTTATATTAAT
Found at i:72079 original size:130 final size:131
Alignment explanation
Indices: 71914--72171 Score: 342
Period size: 131 Copynumber: 2.0 Consensus size: 131
71904 AATAATTTTT
* *
71914 ATAAAACTAATATATATATATATATTTAAGGTTTTATAACTAAGGTATTTATTTATT-TAAAAAT
1 ATAAAACTAAAATATATATATATATTT-AGGTTTTATAACTAAGGTATTTATTTATTAAAAAAAT
* * *
71978 ATCATAAAAGGACATCTAGTTACTTTAAGACAGCCCATTTCTTTAAAATTGAAAAATAAATAAAT
65 ATCAGAAAAGGACATCTAGTTAATTTAAGACAACCC-TTTC-TTAAAATTGAAAAATAAATAAAT
72043 TTGA
128 TTGA
* * *
72047 ATAAAATTAAAAT-TATATATATATTT-GTTTTTATAAGTAAGGTATTTATTTATTAAAAAAATA
1 ATAAAACTAAAATATATATATATATTTAGGTTTTATAACTAAGGTATTTATTTATTAAAAAAATA
* * * * * *
72110 TTAGAATAGGACATCTAGTTAATTTAAGACAATCCTTTCTTAATATTTAGAAATAAATAAAT
66 TCAGAAAAGGACATCTAGTTAATTTAAGACAACCCTTTCTTAAAATTGAAAAATAAATAAAT
72172 ATAAACGATC
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
129 20 0.18
130 30 0.27
131 36 0.33
132 13 0.12
133 11 0.10
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (131 bp):
ATAAAACTAAAATATATATATATATTTAGGTTTTATAACTAAGGTATTTATTTATTAAAAAAATA
TCAGAAAAGGACATCTAGTTAATTTAAGACAACCCTTTCTTAAAATTGAAAAATAAATAAATTTG
A
Found at i:74160 original size:3 final size:3
Alignment explanation
Indices: 74152--74213 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
74142 TTTGGGCTTG
* * *
74152 TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
74198 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
74214 TTTAAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 50 0.96
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:80542 original size:229 final size:227
Alignment explanation
Indices: 80137--80585 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 227
80127 GTAAATTATC
* * *
80137 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
80202 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
80267 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
80332 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
80365 TATCATTTTTATAAAAGTGTCTATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
80430 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* *
80494 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
80559 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
80586 CCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 41 0.20
229 169 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:80673 original size:20 final size:19
Alignment explanation
Indices: 80650--80695 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
80640 CGATATACCA
80650 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
80670 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
80690 GGTAAA
1 GGTAAA
80696 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:80846 original size:19 final size:20
Alignment explanation
Indices: 80815--80860 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
80805 CGATATAACA
80815 GGTAAAAATATGAT-AAACC
1 GGTAAAAATATGATAAAACC
80834 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
80854 GGTAAAA
1 GGTAAAA
80861 TGATACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:83115 original size:21 final size:22
Alignment explanation
Indices: 83078--83118 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
83068 TGCAAAGACA
83078 ATCAAGATCGAAGAGAAACTTG
1 ATCAAGATCGAAGAGAAACTTG
*
83100 ATCAAG-TCGTAGAGAAACT
1 ATCAAGATCGAAGAGAAACT
83119 CGAGAGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (22 bp):
ATCAAGATCGAAGAGAAACTTG
Found at i:83128 original size:21 final size:21
Alignment explanation
Indices: 83085--83145 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
83075 ACAATCAAGA
* *
83085 TCGAAGAGAAACTTGATCA-AG
1 TCGAAGAGAAACTCGA-GAGAG
*
83106 TCGTAGAGAAACTCGAGAGAG
1 TCGAAGAGAAACTCGAGAGAG
* *
83127 TCGAAGATACACTCGAGAG
1 TCGAAGAGAAACTCGAGAG
83146 GAATAAGGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.16
Consensus pattern (21 bp):
TCGAAGAGAAACTCGAGAGAG
Found at i:83221 original size:33 final size:33
Alignment explanation
Indices: 83179--83244 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
83169 AAATAGATGG
*
83179 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
83212 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
83245 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:85060 original size:17 final size:19
Alignment explanation
Indices: 85017--85063 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
85007 AATGTCGAGT
85017 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
85036 TAATTTTGTATACGA-TTA
1 TAATTTTGTATAAGATTTA
85054 T-ATTTTGTAT
1 TAATTTTGTAT
85064 GTGAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
19 14 0.52
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:85716 original size:197 final size:199
Alignment explanation
Indices: 85186--86737 Score: 2887
Period size: 196 Copynumber: 7.9 Consensus size: 199
85176 CAATATGGCC
* *
85186 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAA-
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
85250 CC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
85314 GAATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
85378 TGG-A
195 TGGAA
85382 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
85446 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
85510 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
85575 GGAA
196 GGAA
85579 AACAA-GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
85643 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
85707 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
85772 GGAA
196 GGAA
85776 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
85841 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
85905 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
85970 GG-A
196 GGAA
85973 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
86037 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
86102 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCAATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
86167 GG-A
196 GGAA
86170 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
*
86235 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
86300 GAATATGTCTAAATAATGTGTCGACACTAATAT-GTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
86364 TGGAA
195 TGGAA
86369 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
86432 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
86497 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCCAGAATGAA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTTCCCAGAATGAA
86562 TGGAA
195 TGGAA
86567 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
86631 CAAAAG--TAATGTAATATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
86693 -ATATGTCTAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
86738 AATTTAAATA
Statistics
Matches: 1334, Mismatches: 6, Indels: 36
0.97 0.00 0.03
Matches are distributed among these distances:
192 1 0.00
193 17 0.01
194 12 0.01
195 118 0.09
196 351 0.26
197 339 0.25
198 318 0.24
199 158 0.12
200 20 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAA
Found at i:85942 original size:395 final size:396
Alignment explanation
Indices: 85186--86737 Score: 2879
Period size: 395 Copynumber: 3.9 Consensus size: 396
85176 CAATATGGCC
* *
85186 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAA-
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
85250 CC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
85314 GAATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
85378 TGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGA
195 TGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGA
85443 ACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
260 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
85507 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
325 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
85572 AATGGAA
390 AATGGAA
85579 AACAA-GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
85643 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
85707 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
85772 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCG
85837 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATG
259 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
85901 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
324 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
85966 GAATGG-A
389 GAATGGAA
85973 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
86037 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
86102 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCAATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
86167 GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCC-AAATCATCG
*
86232 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATG
259 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
86297 AGAGAATATGTCTAAATAATGTGTCGACACTAATAT-GTTTGTGTCGATACTTTTTTCCCAGAAT
324 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
86361 GAATGGAA
389 GAATGGAA
86369 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
86432 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
86497 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCCAGAATGAA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTTCCCAGAATGAA
86562 TGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCG
195 TGG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCG
86627 AACCCAAAAG--TAATGTAATATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATG
259 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
86689 AGAG-ATATGTCTAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATACT
324 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
86738 AATTTAAATA
Statistics
Matches: 1138, Mismatches: 6, Indels: 33
0.97 0.01 0.03
Matches are distributed among these distances:
389 2 0.00
390 16 0.01
391 53 0.05
392 102 0.09
393 116 0.10
394 181 0.16
395 494 0.43
396 138 0.12
397 36 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (396 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAA
CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
ATGGAA
Done.