Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003803.1 Hibiscus syriacus cultivar Beakdansim tig00008141_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: 110388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1043 original size:2 final size:2
Alignment explanation
Indices: 1036--1063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1026 TTTTAATCAA
1036 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
1064 TCATGGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1211 original size:16 final size:18
Alignment explanation
Indices: 1170--1212 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1160 TCACGGAATG
1170 TAAGATTACCAGTGAGAA
1 TAAGATTACCAGTGAGAA
*
1188 TAAAATTACCAG-G-GAA
1 TAAGATTACCAGTGAGAA
*
1204 TACGATTAC
1 TAAGATTAC
1213 TGGGAATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
17 1 0.05
18 11 0.50
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (18 bp):
TAAGATTACCAGTGAGAA
Found at i:1370 original size:15 final size:15
Alignment explanation
Indices: 1352--1382 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1342 AAATTCTAAA
1352 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1367 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1382 T
1 T
1383 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2436 original size:30 final size:29
Alignment explanation
Indices: 2402--2462 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
2392 ATTTTTAGTT
* **
2402 GTATTTGTGTTCGTTTATTTATTTTTGAAG
1 GTATTTATGTTCACTTATTT-TTTTTGAAG
*
2432 GTATTTATGTTCACTTATTTTTTTTTAAG
1 GTATTTATGTTCACTTATTTTTTTTGAAG
2461 GT
1 GT
2463 GTTAGTTTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (29 bp):
GTATTTATGTTCACTTATTTTTTTTGAAG
Found at i:6663 original size:21 final size:21
Alignment explanation
Indices: 6634--6686 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6624 ATTCTGAATA
6634 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
6655 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
* *
6676 TCACAATGCGA
1 TCGCATTGCGA
6687 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:6704 original size:20 final size:20
Alignment explanation
Indices: 6679--6748 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
6669 TCCTAATTCA
6679 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
6699 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
6719 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
6739 CAACGCGAAT
1 CAATGCGAAT
6749 CTGACTATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:6966 original size:22 final size:22
Alignment explanation
Indices: 6941--7002 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
6931 ACATCCGTCT
6941 CCATCTCCGACGAAATCAGTCC
1 CCATCTCCGACGAAATCAGTCC
* * *
6963 CCATCTCCAACGATATCAGTCT
1 CCATCTCCGACGAAATCAGTCC
*
6985 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
7003 TTCACGGTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.39, G:0.13, T:0.21
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCC
Found at i:7392 original size:34 final size:33
Alignment explanation
Indices: 7323--7395 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
7313 ACCATCGTAA
** *
7323 TGCGATTCTGTCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAATTCGCGT
7356 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTC-AATTCGCGT
7390 TGCGAT
1 TGCGAT
7396 AGTCATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (33 bp):
TGCGATTCTGTCGTTGCGATAGTCAATTCGCGT
Found at i:7411 original size:20 final size:20
Alignment explanation
Indices: 7368--7435 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
7358 CGATTCTTGC
* *
7368 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGT
* *
7388 GTTGCGATAGTCATTTTTGT
1 GTTGCGATAGTCAATTTCGT
** *
7408 GTTGCGATTTTCAGTTTCGT
1 GTTGCGATAGTCAATTTCGT
7428 GTTGCGAT
1 GTTGCGAT
7436 TTAAAGTTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.43
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGT
Found at i:7443 original size:20 final size:20
Alignment explanation
Indices: 7406--7445 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7396 AGTCATTTTT
**
7406 GTGTTGCGATTTTCAGTTTC
1 GTGTTGCGATTTAAAGTTTC
7426 GTGTTGCGATTTAAAGTTTC
1 GTGTTGCGATTTAAAGTTTC
7446 AGAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.47
Consensus pattern (20 bp):
GTGTTGCGATTTAAAGTTTC
Found at i:9264 original size:20 final size:20
Alignment explanation
Indices: 9239--9433 Score: 197
Period size: 20 Copynumber: 10.5 Consensus size: 20
9229 AGAATAGTTT
9239 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
9259 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
9279 ACTATTGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
9295 A--ATCGCAATGCG--AATG
1 ACTATCGCAATGCGAAAATG
* *
9311 A-AATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
9330 ACTATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
9346 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
9364 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
9384 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
9404 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
9424 ACTATCGCAA
1 ACTATCGCAA
9434 CGAAAGAATC
Statistics
Matches: 150, Mismatches: 10, Indels: 30
0.79 0.05 0.16
Matches are distributed among these distances:
14 13 0.09
15 1 0.01
16 10 0.07
17 16 0.11
18 6 0.04
19 5 0.03
20 99 0.66
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:9445 original size:34 final size:38
Alignment explanation
Indices: 9239--9471 Score: 171
Period size: 40 Copynumber: 6.4 Consensus size: 38
9229 AGAATAGTTT
*
9239 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAA-GCGAAAATGAC-ATCGCAATGCGAAAATG
* *
9279 ACTATTGCAA-CG-AGA-GA-ATCGCAATGCG--AATG
1 ACTATCGCAAGCGAAAATGACATCGCAATGCGAAAATG
*
9311 A-AATCGCAACGCGAAAATGACTATCGCAA--C-AACAA--
1 ACTATCGCAA-GCGAAAATGAC-ATCGCAATGCGAA-AATG
9346 A--ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAA-GCGAAAATGAC-ATCGCAATGCGAAAATG
**
9384 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTG
1 ACTATCGCAA-GCGAAAATGAC-ATCGCAATGCGAAAATG
9424 ACTATCGCAA-CG-AAA-GA-ATCGCAATGCG-AAATG
1 ACTATCGCAAGCGAAAATGACATCGCAATGCGAAAATG
**
9457 AAAATCGCATAGCGA
1 ACTATCGCA-AGCGA
9472 TTCTCTCGTT
Statistics
Matches: 161, Mismatches: 13, Indels: 42
0.75 0.06 0.19
Matches are distributed among these distances:
31 6 0.04
32 5 0.03
33 12 0.07
34 51 0.32
35 6 0.04
36 7 0.04
37 16 0.10
38 5 0.03
40 53 0.33
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.17
Consensus pattern (38 bp):
ACTATCGCAAGCGAAAATGACATCGCAATGCGAAAATG
Found at i:9523 original size:20 final size:20
Alignment explanation
Indices: 9478--9523 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
9468 GCGATTCTCT
9478 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
9498 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
9518 CGTTGC
1 CGTTGC
9524 AATTTTAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:10095 original size:21 final size:20
Alignment explanation
Indices: 10004--10095 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 20
9994 CCCTCACCTG
10004 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
10024 CCTATCGTTCAAGAGGCCCTTA
1 TC-ATCGTTCAAGAGGCCC-TC
** *
10046 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
10067 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
10088 TCATCGTT
1 TCATCGTT
10096 GAGAAGCCCC
Statistics
Matches: 52, Mismatches: 15, Indels: 9
0.68 0.20 0.12
Matches are distributed among these distances:
20 3 0.06
21 42 0.81
22 6 0.12
23 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:11544 original size:14 final size:14
Alignment explanation
Indices: 11525--11578 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
11515 GGAAATGACT
11525 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
11539 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
11558 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
11572 ATCGCAA
1 ATCGCAA
11579 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:11593 original size:34 final size:33
Alignment explanation
Indices: 11505--11600 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
11495 GCAAAAGACT
* **
11505 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
11539 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
11572 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
11601 TGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:11673 original size:19 final size:17
Alignment explanation
Indices: 11648--11700 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
11638 TGCGATTCAC
11648 TCGTTGCGATTTTCATT
1 TCGTTGCGATTTTCATT
*
11665 TCGTTTTGCGA--TTC-TC
1 TCG--TTGCGATTTTCATT
11681 TCGTTGCGATTTTCATT
1 TCGTTGCGATTTTCATT
11698 TCG
1 TCG
11701 CATTGCGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 6 0.21
16 7 0.24
17 10 0.34
19 6 0.21
ACGTcount: A:0.09, C:0.21, G:0.19, T:0.51
Consensus pattern (17 bp):
TCGTTGCGATTTTCATT
Found at i:11684 original size:33 final size:33
Alignment explanation
Indices: 11615--11709 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
11605 ACTAAATTCG
*
11615 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
** *
11649 CGTTGCGATTTTCATTTCGTTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
11682 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
11710 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 41 0.75
34 14 0.25
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:11727 original size:20 final size:20
Alignment explanation
Indices: 11702--11769 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
11692 TTCATTTCGC
11702 ATTGCGATAGTCAATTCCGT
1 ATTGCGATAGTCAATTCCGT
*
11722 ATTGCGATAGTCATTTCCGT
1 ATTGCGATAGTCAATTCCGT
* *
11742 GTTGCGATAGTCATATT-CGC
1 ATTGCGATAGTCA-ATTCCGT
11762 ATTGCGAT
1 ATTGCGAT
11770 TTCCGCGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
ATTGCGATAGTCAATTCCGT
Found at i:13755 original size:22 final size:22
Alignment explanation
Indices: 13711--13755 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13701 TTTTATCCTC
*
13711 TTTGCAATCATATCACGTAGTT
1 TTTGCAATCATATCACCTAGTT
*
13733 TTTGTCAATCATA-CACCTTGTT
1 TTTG-CAATCATATCACCTAGTT
13755 T
1 T
13756 CGAAACGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (22 bp):
TTTGCAATCATATCACCTAGTT
Found at i:13988 original size:14 final size:14
Alignment explanation
Indices: 13969--13995 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13959 TCCCGTAGCA
13969 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
13983 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
13996 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:14932 original size:22 final size:21
Alignment explanation
Indices: 14893--14933 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
14883 TGCCGGATGG
**
14893 GGAAGGATGTCGTTGGATATA
1 GGAAGGATGTCGCCGGATATA
14914 GGAACGGATGTCGCCGGATA
1 GGAA-GGATGTCGCCGGATA
14934 GAGTGATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.12, G:0.39, T:0.22
Consensus pattern (21 bp):
GGAAGGATGTCGCCGGATATA
Found at i:15106 original size:20 final size:20
Alignment explanation
Indices: 15081--15147 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
15071 AAATTCAGTA
15081 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
15101 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
15121 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
15141 TTGCGAT
1 TTGCGAT
15148 TTACGTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:15164 original size:20 final size:20
Alignment explanation
Indices: 15134--15246 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
15124 CGATAGTCAG
*
15134 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
15154 ATTTGCATTGCGAATTACGT
1 ATTCGCATTGCGATTTACGT
15174 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
15194 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
15214 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
15234 ATTCTCATTGCGA
1 ATTCGCATTGCGA
15247 ATTAGGAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:15165 original size:40 final size:39
Alignment explanation
Indices: 15121--15246 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
15111 CAGAATCTCG
*
15121 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTTGCA
1 TTGCGATA-TCAGATTCGCATTGCGATTTACGTATTTGCA
* *
15161 TTGCGA-ATTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATATCA-G-ATTCGCATTGCGATTTACGTATTTGCA
* * *
15201 TTGCGATTTACATATTCACATTGCGATTTACGTATTCT-CA
1 TTGCGATAT-CAGATTCGCATTGCGATTTACGTATT-TGCA
15241 TTGCGA
1 TTGCGA
15247 ATTAGGAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 67 0.92
41 1 0.01
42 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (39 bp):
TTGCGATATCAGATTCGCATTGCGATTTACGTATTTGCA
Found at i:16366 original size:18 final size:18
Alignment explanation
Indices: 16343--16385 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
16333 AGGGAAGATC
*
16343 TTGGAGGAGTGCAGGGAG
1 TTGGAGGAATGCAGGGAG
16361 TTGGAGGAATGCAGGGAG
1 TTGGAGGAATGCAGGGAG
16379 TT-GAGGA
1 TTGGAGGA
16386 TAAATCAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.26, C:0.05, G:0.51, T:0.19
Consensus pattern (18 bp):
TTGGAGGAATGCAGGGAG
Found at i:21519 original size:11 final size:11
Alignment explanation
Indices: 21503--21528 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21493 CCAACCGGAA
21503 TTCGAACTTTC
1 TTCGAACTTTC
21514 TTCGAACTTTC
1 TTCGAACTTTC
21525 TTCG
1 TTCG
21529 GCTACCGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.27, G:0.12, T:0.46
Consensus pattern (11 bp):
TTCGAACTTTC
Found at i:27551 original size:19 final size:19
Alignment explanation
Indices: 27523--27627 Score: 102
Period size: 19 Copynumber: 5.2 Consensus size: 19
27513 GCGATTTTGA
*
27523 AAAATGTGTTGTGATAGTT
1 AAAATGTGTTGCGATAGTT
*
27542 AAAATATGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
27561 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
27581 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
27605 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
27624 AAAA
1 AAAA
27628 ATCCAAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
19 49 0.67
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.14
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:27876 original size:6 final size:6
Alignment explanation
Indices: 27865--27891 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27855 TCTCGTCTCG
27865 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
27892 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:28066 original size:46 final size:45
Alignment explanation
Indices: 28012--28146 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 45
28002 TTAGACTATC
28012 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGAGTT
1 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCG-GTT
28058 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATC----
1 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGGTT
* * * *
28099 GCGTTGCGATTTTGTATTATCGCGTTACGATAGTTAGAATCGCGTT
1 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCG-GTT
28145 GC
1 GC
28147 GATTTACATA
Statistics
Matches: 80, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
41 37 0.46
46 43 0.54
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.37
Consensus pattern (45 bp):
GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGGTT
Found at i:28118 original size:41 final size:41
Alignment explanation
Indices: 28009--28151 Score: 196
Period size: 41 Copynumber: 3.4 Consensus size: 41
27999 AACTTAGACT
28009 ATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGA
28050 ATCGAGTTGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGA
1 ATC-----GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGA
* * * *
28096 ATCGCGTTGCGATTTTGTATTATCGCGTTACGATAGTTAGA
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGA
*
28137 ATCGCGTTGCGATTT
1 ATCGCATTGCGATTT
28152 ACATAGGTCG
Statistics
Matches: 93, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
41 52 0.56
46 41 0.44
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGA
Found at i:28122 original size:21 final size:21
Alignment explanation
Indices: 28061--28151 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 21
28051 TCGAGTTGCA
** *
28061 TTGCGATTTTGTATTATCGCA
1 TTGCGATTTTGTAGAATCGCG
*
28082 TTGCGA--TAGTCAGAATCGCG
1 TTGCGATTTTGT-AGAATCGCG
**
28102 TTGCGATTTTGTATTATCGCG
1 TTGCGATTTTGTAGAATCGCG
* **
28123 TTACGATAGT-TAGAATCGCG
1 TTGCGATTTTGTAGAATCGCG
28143 TTGCGATTT
1 TTGCGATTT
28152 ACATAGGTCG
Statistics
Matches: 52, Mismatches: 15, Indels: 7
0.70 0.20 0.09
Matches are distributed among these distances:
19 3 0.06
20 26 0.50
21 20 0.38
22 3 0.06
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (21 bp):
TTGCGATTTTGTAGAATCGCG
Found at i:28286 original size:21 final size:21
Alignment explanation
Indices: 28262--28305 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
28252 ATTTTCCAAA
*
28262 ATCGCAACGCGATCTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
28283 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
28304 AT
1 AT
28306 TACAACGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:28311 original size:21 final size:21
Alignment explanation
Indices: 28266--28312 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28256 TCCAAAATCG
* *
28266 CAACGCGATCTTGGACTATCG
1 CAACGCGAACTTGGACTATCA
* *
28287 CAACGTGAACTTGGACTATTA
1 CAACGCGAACTTGGACTATCA
28308 CAACG
1 CAACG
28313 AATTTGGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (21 bp):
CAACGCGAACTTGGACTATCA
Found at i:28394 original size:46 final size:46
Alignment explanation
Indices: 28327--28460 Score: 206
Period size: 46 Copynumber: 3.0 Consensus size: 46
28317 TGGAAAATCA
*
28327 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTG
1 CATTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCGTTG
28373 CATTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGC---G
1 CATTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCGTTG
**
28416 --TTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGCGTTG
1 CATTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCGTTG
28460 C
1 C
28461 GATTTACATA
Statistics
Matches: 81, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
41 38 0.47
43 1 0.01
44 1 0.01
46 41 0.51
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (46 bp):
CATTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCGTTG
Found at i:28422 original size:20 final size:20
Alignment explanation
Indices: 28399--28463 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
28389 TATCGCATTA
28399 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
* ** * *
28419 CGATTTTGT-ATTATCGTGTTA
1 CGA--TAGTCAGAATCGCGTTG
28440 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
28460 CGAT
1 CGAT
28464 TTACATAGGT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
21 11 0.34
22 3 0.09
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (20 bp):
CGATAGTCAGAATCGCGTTG
Found at i:28432 original size:41 final size:41
Alignment explanation
Indices: 28329--28465 Score: 202
Period size: 41 Copynumber: 3.2 Consensus size: 41
28319 GAAAATCACA
*
28329 TTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTG
1 TTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGC---G
28373 CATTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCG
1 --TTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCG
**
28416 TTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGCG
1 TTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCG
28457 TTGCGATTT
1 TTGCGATTT
28466 ACATAGGTCG
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
41 48 0.55
43 1 0.01
46 39 0.44
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCATTACGATAGTCAGAATCGCG
Found at i:28434 original size:21 final size:21
Alignment explanation
Indices: 28378--28443 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
28368 CGTTGCATTG
*
28378 CGATTTTGTATTATCGCATTA
1 CGATTTTGTATTATCGCGTTA
* ** *
28399 CGA--TAGTCAGAATCGCGTTG
1 CGATTTTGT-ATTATCGCGTTA
*
28419 CGATTTTGTATTATCGTGTTA
1 CGATTTTGTATTATCGCGTTA
28440 CGAT
1 CGAT
28444 AGTCAGAATC
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 15 0.47
22 3 0.09
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (21 bp):
CGATTTTGTATTATCGCGTTA
Found at i:28582 original size:314 final size:314
Alignment explanation
Indices: 28013--28784 Score: 1431
Period size: 314 Copynumber: 2.5 Consensus size: 314
28003 TAGACTATCG
*
28013 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGAGTTGCATTGCGATTTTGTATTAT
1 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTGCATTGCGATTTTGTATTAT
* * *
28078 CGCATTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGCGTTACGATAGTTAGAATCGCG
66 CGCATTACGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGCG
*
28143 TTGCGATTTACATAGGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCGGATACTATCTTTTTA
131 TTGCGATTTACATAGGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCAGATACTATCTTTTTA
*
28208 GAGAAATTTCTTAAGAAACAAATGCAATGCCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCG
196 GAGAAATTTCTTAAGAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCG
*
28273 -ATCTTGGACTATCGCAACGTGAACTTGGACTATTACAACGAATTTGGAAAATCA
261 AAT-TTGGACTATCGCAACGTGAACTTGGACTATCACAACGAATTTGGAAAATCA
28327 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTGCATTGCGATTTTGTATTAT
1 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTGCATTGCGATTTTGTATTAT
28392 CGCATTACGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGCG
66 CGCATTACGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGCG
28457 TTGCGATTTACATAGGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCAGATACTATCTTTTTA
131 TTGCGATTTACATAGGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCAGATACTATCTTTTTA
28522 GAGAAATTTCTTAAGAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCG
196 GAGAAATTTCTTAAGAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCG
* *
28587 AATTTGGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCG
261 AATTTGGACTATCGCAACGTGAACTTGGACTATCACAACGAATTTGGAAAATCA
28641 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTGCATTGCGATTTTGTATTAT
1 CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTGCATTGCGATTTTGTATTAT
28706 CGCATTGA-GATAGTCAGAATCGCGTTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGC
66 CGCATT-ACGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGC
28770 GTTGCGATTTACATA
130 GTTGCGATTTACATA
28785 TTTGCATTGC
Statistics
Matches: 447, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
314 444 0.99
315 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (314 bp):
CATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTTGCATTGCGATTTTGTATTAT
CGCATTACGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGCG
TTGCGATTTACATAGGTCGTGGTAATACGTGTCTTCGACACGTCCGCGCAGATACTATCTTTTTA
GAGAAATTTCTTAAGAAACAAATGCAATACCACCAGTCGTTGCGATTTTCCAAAATCGCAACGCG
AATTTGGACTATCGCAACGTGAACTTGGACTATCACAACGAATTTGGAAAATCA
Found at i:28600 original size:21 final size:21
Alignment explanation
Indices: 28576--28634 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
28566 ATTTTCCAAA
28576 ATCGCAACGCGAATTTGGACT
1 ATCGCAACGCGAATTTGGACT
* *
28597 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAATTTGGACT
28618 ATCGCAA--CGAATTTGGA
1 ATCGCAACGCGAATTTGGA
28635 AAATCGCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.24
21 26 0.76
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGAATTTGGACT
Found at i:28640 original size:19 final size:19
Alignment explanation
Indices: 28573--28642 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 19
28563 GCGATTTTCC
28573 AAAATCGCAACGCGAATTTGG
1 AAAATCGCAA--CGAATTTGG
** *
28594 ACTATCGCAACGTGAACTTGG
1 AAAATCGCAAC--GAATTTGG
**
28615 ACTATCGCAACGAATTTGG
1 AAAATCGCAACGAATTTGG
28634 AAAATCGCA
1 AAAATCGCA
28643 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 15 0.37
21 26 0.63
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAATCGCAACGAATTTGG
Found at i:28707 original size:46 final size:46
Alignment explanation
Indices: 28640--28774 Score: 199
Period size: 46 Copynumber: 3.0 Consensus size: 46
28630 TTGGAAAATC
28640 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTT
1 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTT
*
28686 GCATTGCGATTTTGTATTATCGCATTGAGATAGTCAGAATCGC---
1 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTT
** *
28729 G--TTGCGATTTTGTATTATCGTGTTACGATAGTCAGAATCGCGTT
1 GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTT
28773 GC
1 GC
28775 GATTTACATA
Statistics
Matches: 80, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
41 36 0.45
43 1 0.01
44 1 0.01
46 42 0.52
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.37
Consensus pattern (46 bp):
GCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGAATCGCGTT
Found at i:28712 original size:21 final size:21
Alignment explanation
Indices: 28686--28748 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
28676 GAATCGCGTT
28686 GCATTGCGATTTTGTATTATC
1 GCATTGCGATTTTGTATTATC
* * **
28707 GCATTGAGA--TAGTCAGAATC
1 GCATTGCGATTTTGT-ATTATC
*
28727 GCGTTGCGATTTTGTATTATC
1 GCATTGCGATTTTGTATTATC
28748 G
1 G
28749 TGTTACGATA
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 13 0.43
22 3 0.10
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (21 bp):
GCATTGCGATTTTGTATTATC
Found at i:28746 original size:41 final size:41
Alignment explanation
Indices: 28636--28816 Score: 206
Period size: 41 Copynumber: 4.3 Consensus size: 41
28626 GAATTTGGAA
* *
28636 AATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCATTGAGATAGTCAG
28677 AATCGCGTTGCATTGCGATTTTGTATTATCGCATTGAGATAGTCAG
1 AATCGC---G--TTGCGATTTTGTATTATCGCATTGAGATAGTCAG
**
28723 AATCGCGTTGCGATTTTGTATTATCGTGTT-ACGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCATTGA-GATAGTCAG
** * *
28764 AATCGCGTTGCGATTTACATATT-T-GCATTGCGATAGTCAA
1 AATCGCGTTGCGATTT-TGTATTATCGCATTGAGATAGTCAG
28804 AATCGCGTTGCGA
1 AATCGCGTTGCGA
28817 ATCTGGAAAC
Statistics
Matches: 122, Mismatches: 10, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
40 25 0.20
41 53 0.43
42 4 0.03
43 1 0.01
46 39 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTGTATTATCGCATTGAGATAGTCAG
Found at i:28777 original size:20 final size:20
Alignment explanation
Indices: 28704--28816 Score: 68
Period size: 20 Copynumber: 5.6 Consensus size: 20
28694 ATTTTGTATT
* *
28704 ATCGCATTGAGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
28724 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
* *
28745 ATCGTGTTACGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
28765 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * * *
28785 TTTGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
28805 ATCGCGTTGCGA
1 ATCGCGTTGCGA
28817 ATCTGGAAAC
Statistics
Matches: 66, Mismatches: 22, Indels: 10
0.67 0.22 0.10
Matches are distributed among these distances:
19 4 0.06
20 47 0.71
21 12 0.18
22 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:28854 original size:20 final size:19
Alignment explanation
Indices: 28831--28876 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28821 GGAAACTGAT
* *
28831 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
28851 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
28870 TTGCGAT
1 TTGCGAT
28877 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:28866 original size:19 final size:19
Alignment explanation
Indices: 28842--28878 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28832 TGCGATACTG
*
28842 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
28861 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
28879 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:29133 original size:60 final size:60
Alignment explanation
Indices: 29022--29134 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
29012 TATAGGGTAG
* * ** ***
29022 TACTTTATTAAGTTCCTCAACTATTAAAAGTTATAAAATTATCATTTGACTATATAATGA
1 TACTTTATTAAATCCCTCAACTATTAAAAGTTATAAAACGATCACCCGACTATATAATGA
* *
29082 TACTTTGTTAAATCCCTTAACTATTAAAAGTTATAAAACGATCACCCGACTAT
1 TACTTTATTAAATCCCTCAACTATTAAAAGTTATAAAACGATCACCCGACTAT
29135 TTATTATGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (60 bp):
TACTTTATTAAATCCCTCAACTATTAAAAGTTATAAAACGATCACCCGACTATATAATGA
Found at i:31013 original size:3 final size:3
Alignment explanation
Indices: 31005--31059 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
30995 GGTTGGGTTC
31005 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
31053 TCT TCT T
1 TCT TCT T
31060 GTCGTTCCCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:31615 original size:21 final size:19
Alignment explanation
Indices: 31583--31622 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
31573 TGAAGAAATA
31583 CGATGAATAGTATCGATAC
1 CGATGAATAGTATCGATAC
31602 CGATGCAATTAGTATCGATAC
1 CGATG-AA-TAGTATCGATAC
31623 TAATGTGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (19 bp):
CGATGAATAGTATCGATAC
Found at i:32160 original size:54 final size:54
Alignment explanation
Indices: 32091--32481 Score: 435
Period size: 54 Copynumber: 7.3 Consensus size: 54
32081 GTGTGTAATT
* * *
32091 TAAGAAATTCATAATAAGTTTATGAATGTT-TGTATTGGCACTGTGTGTGCAACT
1 TAAGAAATTCATAATAAGTTTATGAAT-TTCCGTATTGGCACTATGTGTGCAACC
* * * *
32145 TAAGAAATTCATAATAAGTTTATGAATTTCCATATTGACACTCTGTGTGCAACT
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACC
* * * *
32199 TAAGAAAATCATAATAAGTTTATGAATTTCTGTATTGGCACTGTGTGTGGAACC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACC
* *
32253 TAAGAAATTAATAATAAGTTTATGAATTT-TGTATTGGCACTATGTGTGCAACC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACC
* *
32306 TAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTATGTGTGCACCC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACC
* * * * * * ** *
32360 CATGTAATTCATAATGAGTTTGTGAATTACCGTATCAGCACTAAGTGTGCAACC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACC
* * * ** * * * *
32414 CACGAAATTCATTATAAGTTTATGAATGACCGTATCGACACTAAGTGTTCAACC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACC
* * *
32468 CATGGAATTCATAA
1 TAAGAAATTCATAA
32482 CGAGCTTATT
Statistics
Matches: 294, Mismatches: 41, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 51 0.17
54 243 0.83
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (54 bp):
TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACC
Found at i:32374 original size:161 final size:162
Alignment explanation
Indices: 32091--32441 Score: 470
Period size: 161 Copynumber: 2.2 Consensus size: 162
32081 GTGTGTAATT
* *
32091 TAAGAAATTCATAATAAGTTTATGAATGTTTGTATTGGCACTGTGTGTGCAACTTAAGAAATTCA
1 TAAGAAATTCATAATAAGTTTATGAATGTTTGTATTGGCACTATGTGTGCAACCTAAGAAATTCA
* **
32156 TAATAAGTTTATGAATTTCCATATTGACACTCTGTGTGCAACTTAAGAAAATCATAATAAGTTTA
66 TAATAAGTTTATGAATTTCCATATTGACACTATGTGTGCAACCCAAGAAAATCATAATAAGTTTA
* * ** ** *
32221 TGAATTTCTGTATTGGCACTGTGTGTGGAACC
131 TGAATTACCGTATCAGCACTAAGTGTGCAACC
*
32253 TAAGAAATTAATAATAAGTTTATGAAT-TTTGTATTGGCACTATGTGTGCAACCTAAGAAATTCA
1 TAAGAAATTCATAATAAGTTTATGAATGTTTGTATTGGCACTATGTGTGCAACCTAAGAAATTCA
* * * * * * * * *
32317 TAATTAGTTTATGAATTTCCGTATTGGCACTATGTGTGCACCCCATGTAATTCATAATGAGTTTG
66 TAATAAGTTTATGAATTTCCATATTGACACTATGTGTGCAACCCAAGAAAATCATAATAAGTTTA
32382 TGAATTACCGTATCAGCACTAAGTGTGCAACC
131 TGAATTACCGTATCAGCACTAAGTGTGCAACC
* * *
32414 CACGAAATTCATTATAAGTTTATGAATG
1 TAAGAAATTCATAATAAGTTTATGAATG
32442 ACCGTATCGA
Statistics
Matches: 162, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
161 136 0.84
162 26 0.16
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (162 bp):
TAAGAAATTCATAATAAGTTTATGAATGTTTGTATTGGCACTATGTGTGCAACCTAAGAAATTCA
TAATAAGTTTATGAATTTCCATATTGACACTATGTGTGCAACCCAAGAAAATCATAATAAGTTTA
TGAATTACCGTATCAGCACTAAGTGTGCAACC
Found at i:38059 original size:54 final size:54
Alignment explanation
Indices: 37971--38446 Score: 465
Period size: 54 Copynumber: 8.9 Consensus size: 54
37961 ATTTACCGAA
* *
37971 TGACACTATGTGTGCAATTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
38025 TGGCATTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
1 TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * * *
38079 TGGCACTGCGTGTGCAACATAAGAAACTCATAATAAGTTTATGAATTTTCGTAT
1 TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
38133 TGACACTGTTTGTGCAACTTAAGAAATTCATAATAAGTTTATGAACTTCCGAAT
1 TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
38187 TGACA--GTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * **
38239 TAACACTATGTGTGCAACCTGAA-AAATTCATAATTTGTTTATGAATTTCCGTAT
1 TGACACTGTGTGTGCAA-CTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * * ** * * * * ** *
38293 TGGCATTATGTGTGCACCCCATGTAATTCATAATGAGTTTGTGAATTAACATAT
1 TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * ** * * ***
38347 CGCCACTAAGTGTGCAACTCACAG-AATCCATAATAAGTTTATGAACGACCGTAT
1 TGACACTGTGTGTGCAACTTA-AGAAATTCATAATAAGTTTATGAATTTCCGTAT
* ** *** * * *
38401 CGACACTAAGTGTGCAACTCGTGGAATTCATAATGAGCTTATGAAT
1 TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAAT
38447 GACTGTATCG
Statistics
Matches: 354, Mismatches: 62, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
52 48 0.14
53 3 0.01
54 298 0.84
55 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (54 bp):
TGACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
Found at i:38323 original size:160 final size:161
Alignment explanation
Indices: 37971--38337 Score: 459
Period size: 160 Copynumber: 2.3 Consensus size: 161
37961 ATTTACCGAA
*** * * *
37971 TGACACTATGTGTGCAATTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCATTGTGT
1 TGACACTATGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAACTTCCGAATTGACA-TGTGT
* ** *
38036 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTGCGTGTGCAACATAA
65 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTACGTGTGCAACATAA
*
38101 GAAACTCATAATAAGTTTATGAATTTTCGTAT
130 GAAACTCATAATAAGTTTATGAATTTCCGTAT
* * **
38133 TGACACTGTTTGTGCAACTTAAGAAATTCATAATAAGTTTATGAACTTCCGAATTGACA-GTGTG
1 TGACACTATGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAACTTCCGAATTGACATGTGTG
* *
38197 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTATGTGTGCAACCTGAA
66 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTACGTGTGCAACAT-AA
* **
38262 -AAATTCATAATTTGTTTATGAATTTCCGTAT
130 GAAACTCATAATAAGTTTATGAATTTCCGTAT
* * * * * * *
38293 TGGCATTATGTGTGCACCCCATGTAATTCATAATGAGTTTGTGAA
1 TGACACTATGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAA
38338 TTAACATATC
Statistics
Matches: 177, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
160 122 0.69
161 2 0.01
162 53 0.30
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (161 bp):
TGACACTATGTGTGCAACCCAAGAAATTCATAATAAGTTTATGAACTTCCGAATTGACATGTGTG
TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTACGTGTGCAACATAAG
AAACTCATAATAAGTTTATGAATTTCCGTAT
Found at i:38363 original size:214 final size:214
Alignment explanation
Indices: 37979--38392 Score: 526
Period size: 214 Copynumber: 1.9 Consensus size: 214
37969 AATGACACTA
* ** * *
37979 TGTGTGCAATTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCATTGTGTGTGCAACT
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTATGTGTGCAACT
* * * *
38044 TAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTGCGTGTGCAACATAAGAAACTCA
66 GAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTACGTGTGCAACACAAGAAACTCA
** * * *** * *
38109 TAATAAGTTTATGAATTTTCGTATTGACACTGTTTGTGCAACTTA-AGAAATTCATAATAAGTTT
131 TAATAAGTTTATGAATTAACATATCGACACTAAGTGTGCAACTCACAG-AATCCATAATAAGTTT
38173 ATGAACTTCCGAATTGACAG
195 ATGAACTTCCGAATTGACAG
38193 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTATGTGTGCAACC
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTATGTGTGCAA-C
** * * * * * * *
38258 TGAA-AAATTCATAATTTGTTTATGAATTTCCGTATTGGCATTATGTGTGCACCCCATGTAATTC
65 TGAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTACGTGTGCAACACAAGAAACTC
* * *
38322 ATAATGAGTTTGTGAATTAACATATCGCCACTAAGTGTGCAACTCACAGAATCCATAATAAGTTT
130 ATAATAAGTTTATGAATTAACATATCGACACTAAGTGTGCAACTCACAGAATCCATAATAAGTTT
38387 ATGAAC
195 ATGAAC
38393 GACCGTATCG
Statistics
Matches: 168, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
214 162 0.96
215 6 0.04
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (214 bp):
TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAACACTATGTGTGCAACT
GAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTACGTGTGCAACACAAGAAACTCA
TAATAAGTTTATGAATTAACATATCGACACTAAGTGTGCAACTCACAGAATCCATAATAAGTTTA
TGAACTTCCGAATTGACAG
Found at i:42356 original size:22 final size:20
Alignment explanation
Indices: 42331--42370 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42321 TAAATTTTAT
*
42331 GATTTAAGATTTTAATGATTAG
1 GATTT-AGACTTT-ATGATTAG
42353 GATTTAGACTTTATGATT
1 GATTTAGACTTTATGATT
42371 TATAATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (20 bp):
GATTTAGACTTTATGATTAG
Found at i:63829 original size:34 final size:34
Alignment explanation
Indices: 63756--63832 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
63746 GGATTATATT
* * *
63756 TATTATTTTATTAGGAATTAAGAAAGATTTAAAA
1 TATTATCTTATTAGGAATTAAGAAAGAATCAAAA
*
63790 CATTATCTTATTAGGAATT-AGAATAGAATCAAAA
1 TATTATCTTATTAGGAATTAAGAA-AGAATCAAAA
63824 TATTATCTT
1 TATTATCTT
63833 TAGTTTATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 4 0.11
34 33 0.89
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.40
Consensus pattern (34 bp):
TATTATCTTATTAGGAATTAAGAAAGAATCAAAA
Found at i:69171 original size:15 final size:15
Alignment explanation
Indices: 69148--69180 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
69138 CATTACCCGC
*
69148 CCCCGCATCCGCCCA
1 CCCCACATCCGCCCA
69163 CCCCACATCCGCCCA
1 CCCCACATCCGCCCA
69178 CCC
1 CCC
69181 AGCTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.70, G:0.09, T:0.06
Consensus pattern (15 bp):
CCCCACATCCGCCCA
Found at i:69315 original size:12 final size:12
Alignment explanation
Indices: 69298--69324 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
69288 TATTAAGGAT
69298 ATTTAGTCTTTA
1 ATTTAGTCTTTA
69310 ATTTAGTCTTTA
1 ATTTAGTCTTTA
69322 ATT
1 ATT
69325 AGGGAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (12 bp):
ATTTAGTCTTTA
Found at i:74316 original size:35 final size:35
Alignment explanation
Indices: 74277--74392 Score: 101
Period size: 35 Copynumber: 3.1 Consensus size: 35
74267 GAGAATTGAC
*
74277 AGTGTTATGCCTTCTTTCGTTCTACTTGAATCAAA
1 AGTGTTATGCCTTCTTTCGTTCTACTTGAATCGAA
* *
74312 AGTGTGATG-CTTACTTCCGTTCTACTTTAGATAAAAATCGAA
1 AGTGTTATGCCTT-CTTTCGTTCTAC-TT-G-----AATCGAA
*
74354 AGTGTTATGCCTCCGTTT-GTTCTACTTGAATCGAA
1 AGTGTTATGCCTTC-TTTCGTTCTACTTGAATCGAA
74389 AGTG
1 AGTG
74393 CGATGCTTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
34 3 0.05
35 30 0.46
36 2 0.03
37 1 0.02
40 1 0.02
41 2 0.03
42 22 0.34
43 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (35 bp):
AGTGTTATGCCTTCTTTCGTTCTACTTGAATCGAA
Found at i:74335 original size:77 final size:77
Alignment explanation
Indices: 74187--74495 Score: 345
Period size: 77 Copynumber: 4.0 Consensus size: 77
74177 TTTTGTCATC
* * * * * *
74187 GAGAATCGAAAGTGCTATGCC-TCTTTTTGCTCTACTTTAATCGAAAAAAGTACGATGCTTCCTT
1 GAGAATTGAAAGTGTTATGCCTTC-TTTCGTTCTACTTGAATC---AAAAGTGCGATGCTTCCTT
74251 CCATTCTACTTTAGAT
62 CCATTCTACTTTAGAT
* * * *
74267 GAGAATTGACAGTGTTATGCCTTCTTTCGTTCTACTTGAATCAAAAGTGTGATGCTTACTTCCGT
1 GAGAATTGAAAGTGTTATGCCTTCTTTCGTTCTACTTGAATCAAAAGTGCGATGCTTCCTTCCAT
74332 TCTACTTTAGAT
66 TCTACTTTAGAT
* * * * *
74344 AAAAATCGAAAGTGTTATGCCTCCGTTT-GTTCTACTTGAATCGAAAGTGCGATGCTTCCTTCCA
1 GAGAATTGAAAGTGTTATGCCTTC-TTTCGTTCTACTTGAATCAAAAGTGCGATGCTTCCTTCCA
74408 TTCTACTTTAGAT
65 TTCTACTTTAGAT
* * * * **
74421 GAGAATTGAAAGTGCTATACC-TCCTTCTGTTATGTTTGAATCGAAAAGTGCGATGCTTCCTTCC
1 GAGAATTGAAAGTGTTATGCCTTCTTTC-GTTCTACTTGAATC-AAAAGTGCGATGCTTCCTTCC
74485 ATTCTACTTTA
64 ATTCTACTTTA
74496 TTCGCCTTTC
Statistics
Matches: 194, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
75 2 0.01
76 1 0.01
77 122 0.63
78 34 0.18
80 33 0.17
81 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (77 bp):
GAGAATTGAAAGTGTTATGCCTTCTTTCGTTCTACTTGAATCAAAAGTGCGATGCTTCCTTCCAT
TCTACTTTAGAT
Found at i:74421 original size:154 final size:156
Alignment explanation
Indices: 74190--74495 Score: 420
Period size: 154 Copynumber: 2.0 Consensus size: 156
74180 TGTCATCGAG
** *
74190 AATCGAAAGTGCTATGCCTCTTTTTGCTCTACTTTAATCGAAAAAAGTACGATGCTTCCTTCCAT
1 AATCGAAAGTGCTATGCCTCCGTTTGCTCTACTTGAATCG--AAAAGTACGATGCTTCCTTCCAT
* * * * * *
74255 TCTACTTTAGATGAGAATTGACAGTGTTATGCCTTCTT-TCGTTCTACTTGAATC-AAAAGTGTG
64 TCTACTTTAGATGAGAATTGAAAGTGCTATACCTCCTTCT-GTTATACTTGAATCGAAAAGTGCG
*
74318 ATGCTTACTTCCGTTCTACTTTAGATAAA
128 ATGCTTACTTCCATTCTACTTTAGATAAA
* * *
74347 AATCGAAAGTGTTATGCCTCCGTTTGTTCTACTTGAATCG-AAAGTGCGATGCTTCCTTCCATTC
1 AATCGAAAGTGCTATGCCTCCGTTTGCTCTACTTGAATCGAAAAGTACGATGCTTCCTTCCATTC
**
74411 TACTTTAGATGAGAATTGAAAGTGCTATACCTCCTTCTGTTATGTTTGAATCGAAAAGTGCGATG
66 TACTTTAGATGAGAATTGAAAGTGCTATACCTCCTTCTGTTATACTTGAATCGAAAAGTGCGATG
*
74476 CTTCCTTCCATTCTACTTTA
131 CTTACTTCCATTCTACTTTA
74496 TTCGCCTTTC
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
154 66 0.50
155 30 0.23
157 35 0.27
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (156 bp):
AATCGAAAGTGCTATGCCTCCGTTTGCTCTACTTGAATCGAAAAGTACGATGCTTCCTTCCATTC
TACTTTAGATGAGAATTGAAAGTGCTATACCTCCTTCTGTTATACTTGAATCGAAAAGTGCGATG
CTTACTTCCATTCTACTTTAGATAAA
Found at i:75289 original size:18 final size:18
Alignment explanation
Indices: 75260--75328 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
75250 AATATTTGTT
*
75260 CCGAATGACCACTATGTC
1 CCGAAGGACCACTATGTC
* *
75278 CCAAAGGACCACTGATTGTT
1 CCGAAGGACCACT-A-TGTC
* *
75298 CCGAAGAACCACCATGTC
1 CCGAAGGACCACTATGTC
75316 CCGAAGGACCACT
1 CCGAAGGACCACT
75329 GATAATCCCT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 25 0.62
19 2 0.05
20 13 0.32
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
CCGAAGGACCACTATGTC
Found at i:75300 original size:38 final size:38
Alignment explanation
Indices: 75255--75331 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
75245 CACTGAATAT
*
75255 TTGTTCCGAATG-ACCACTATGTCCCAAAGGACCACTGA
1 TTGTTCCGAA-GAACCACCATGTCCCAAAGGACCACTGA
*
75293 TTGTTCCGAAGAACCACCATGTCCCGAAGGACCACTGA
1 TTGTTCCGAAGAACCACCATGTCCCAAAGGACCACTGA
75331 T
1 T
75332 AATCCCTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (38 bp):
TTGTTCCGAAGAACCACCATGTCCCAAAGGACCACTGA
Found at i:75974 original size:64 final size:64
Alignment explanation
Indices: 75899--76038 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 64
75889 ATCCCTTGAT
* * *
75899 GGGTGCATCGATGCACAA-TCTATGCATCGGTACA-TAAATCCCATTCAATGTTTTTATTTTAAG
1 GGGTGCATCGATGCACAACT-TATGCATCGATACACT-AATCACATTCAATGTTTTTATTTTAAA
75962 G
64 G
* * * * *
75963 GGGTGCATCGATGCACTACTTGTGCATTGATACACTAATGACATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACAACTTATGCATCGATACACTAATCACATTCAATGTTTTTATTTTAAAG
*
76027 GAGTGCATCGAT
1 GGGTGCATCGAT
76039 ACACCTCATG
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 63 0.97
65 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACAACTTATGCATCGATACACTAATCACATTCAATGTTTTTATTTTAAAG
Found at i:81302 original size:6 final size:6
Alignment explanation
Indices: 81291--81325 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
81281 CTGACTTCTT
*
81291 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTT CCTCT
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCT
81326 CTGGGTAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (6 bp):
CCTCTA
Found at i:85381 original size:19 final size:19
Alignment explanation
Indices: 85357--85432 Score: 116
Period size: 19 Copynumber: 4.0 Consensus size: 19
85347 TTTAAGCAGG
85357 TGCATCGATGCACTCATTA
1 TGCATCGATGCACTCATTA
*
85376 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCATTA
* *
85395 TGCATCGATACACTCCTTA
1 TGCATCGATGCACTCATTA
*
85414 TGCATCGATGCACTAATTA
1 TGCATCGATGCACTCATTA
85433 CATTCGATGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCATTA
Found at i:91454 original size:20 final size:18
Alignment explanation
Indices: 91411--91479 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
91401 AATATTTATC
91411 CCGAAGGACCACTATGTA
1 CCGAAGGACCACTATGTA
* *
91429 CCGAAGGACCACTGATTTTT
1 CCGAAGGACCACT-A-TGTA
*
91449 CCGAAGAACCACTATGT-
1 CCGAAGGACCACTATGTA
*
91466 CCTGAAAGACCACT
1 CC-GAAGGACCACT
91480 CCTTAAGAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.05
18 24 0.57
19 2 0.05
20 14 0.33
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (18 bp):
CCGAAGGACCACTATGTA
Found at i:91725 original size:2 final size:2
Alignment explanation
Indices: 91720--91795 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
91710 TATACACACA
91720 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
91762 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
91796 GATGCATGTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:92194 original size:19 final size:19
Alignment explanation
Indices: 92166--92216 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
92156 TGTATTTTAA
92166 GCATCGATGCACTCCTTAT
1 GCATCGATGCACTCCTTAT
*
92185 GCATCAATGCACTCCTTAT
1 GCATCGATGCACTCCTTAT
92204 GCATCGATGCACT
1 GCATCGATGCACT
92217 AATTGCATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (19 bp):
GCATCGATGCACTCCTTAT
Found at i:95577 original size:15 final size:17
Alignment explanation
Indices: 95557--95588 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
95547 CATAATATAA
95557 TAAA-TTCAAG-TAGAT
1 TAAATTTCAAGATAGAT
95572 TAAATTTCAAGATAGAT
1 TAAATTTCAAGATAGAT
95589 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 6 0.40
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (17 bp):
TAAATTTCAAGATAGAT
Found at i:97630 original size:32 final size:31
Alignment explanation
Indices: 97594--97678 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
97584 TAGGCCCTGC
97594 GGCCCTAAGATGTGTTCTTAGGTAGGC-CCCA
1 GGCCCTAAGATGT-TTCTTAGGTAGGCTCCCA
* * * * *
97625 TGGCCCCAAAATCTTTCTTGGGTAGGCTCTCA
1 -GGCCCTAAGATGTTTCTTAGGTAGGCTCCCA
97657 GGCCCTAAGATGTTCTCTTAGG
1 GGCCCTAAGATGTT-TCTTAGG
97679 GTAACTATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
31 23 0.55
32 19 0.45
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (31 bp):
GGCCCTAAGATGTTTCTTAGGTAGGCTCCCA
Found at i:99192 original size:30 final size:30
Alignment explanation
Indices: 99151--99213 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
99141 ACGTAGGCAG
99151 GTGGTAGCCCTTCAAGATGAGATTTTTGAT
1 GTGGTAGCCCTTCAAGATGAGATTTTTGAT
* *
99181 GTGGTATCCCTTCAAGATGAGATTTTTTAT
1 GTGGTAGCCCTTCAAGATGAGATTTTTGAT
99211 GTG
1 GTG
99214 CTGGTGAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (30 bp):
GTGGTAGCCCTTCAAGATGAGATTTTTGAT
Found at i:103958 original size:13 final size:13
Alignment explanation
Indices: 103928--103962 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
103918 GACCGGTTCG
*
103928 ACCCGACCCGTTG
1 ACCCGACCCGTTA
103941 A-CCGACCCGTTA
1 ACCCGACCCGTTA
103953 ACCCGACCCG
1 ACCCGACCCG
103963 ACCCGGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.11
Consensus pattern (13 bp):
ACCCGACCCGTTA
Found at i:105081 original size:25 final size:25
Alignment explanation
Indices: 105029--105081 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
105019 AGGGTAACTC
*
105029 TTTTATGAGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
105054 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
105079 TTT
1 TTT
105082 ATTTAATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:106901 original size:32 final size:33
Alignment explanation
Indices: 106865--106943 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
106855 TTTCAATATG
** *
106865 TTCGGGTTGCTTTTGGGTCAGGTT-AAATTCGA
1 TTCGGGTTGCTTTCAGATCAGGTTAAAATTCGA
*
106897 TTCGGGTTGCTTTCAGATCGGGTTAAAATTCGA
1 TTCGGGTTGCTTTCAGATCAGGTTAAAATTCGA
* *
106930 TTCAGGTTTCTTTC
1 TTCGGGTTGCTTTC
106944 GGTTCGGGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 20 0.50
33 20 0.50
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (33 bp):
TTCGGGTTGCTTTCAGATCAGGTTAAAATTCGA
Found at i:106931 original size:33 final size:33
Alignment explanation
Indices: 106865--106955 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
106855 TTTCAATATG
* * *
106865 TTCGGGTTGCTTTTGGGTCAGGTT-AAATTCGA
1 TTCGGGTTGCTTTCGGATCGGGTTAAAATTCGA
*
106897 TTCGGGTTGCTTTCAGATCGGGTTAAAATTCGA
1 TTCGGGTTGCTTTCGGATCGGGTTAAAATTCGA
* * *
106930 TTCAGGTTTCTTTCGGTTCGGGTTAA
1 TTCGGGTTGCTTTCGGATCGGGTTAA
106956 TTTTGGATCG
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
32 20 0.40
33 30 0.60
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (33 bp):
TTCGGGTTGCTTTCGGATCGGGTTAAAATTCGA
Found at i:107395 original size:14 final size:14
Alignment explanation
Indices: 107374--107415 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
107364 TAGTTCTCTT
107374 TATA-TATCCATTA
1 TATATTATCCATTA
107387 TATATTATCCATTA
1 TATATTATCCATTA
* * *
107401 TCTTTTAACCATTA
1 TATATTATCCATTA
107415 T
1 T
107416 TTTTTTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTATCCATTA
Found at i:109341 original size:2 final size:2
Alignment explanation
Indices: 109334--109398 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
109324 ACGTTTTATT
109334 TA TA TA TA TA TA TA TA TA TA TA TA -A 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 TA TA TA TA TA
*
109374 TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
109399 GTATTTGTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.