Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007476.1 Hibiscus syriacus cultivar Beakdansim tig00020562_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: 59468
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1565 original size:21 final size:21
Alignment explanation
Indices: 1541--1593 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1531 ATTCTGACTA
1541 TCGCATTGCGA-TTTCTCAAAT
1 TCGCATTGCGATTTTC-CAAAT
* *
1562 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1583 TCGCAATGCGA
1 TCGCATTGCGA
1594 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1608 original size:20 final size:20
Alignment explanation
Indices: 1583--1674 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
1573 TTTTCCTAAT
1583 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1603 TCGCAACGCG-ATA-GGAAA
1 TCGCAATGCGAATACGTAAA
* *
1621 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1642 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1662 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1675 CGACTATCGT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.21
19 4 0.06
20 30 0.48
21 16 0.25
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1671 original size:41 final size:39
Alignment explanation
Indices: 1583--1674 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 39
1573 TTTTCCTAAT
*
1583 TCGCAATGCGAA-TACGTAAATCGCAACGCGATAGGAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGATAGGAAA
* * *
1621 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCG-ATA-GGAAA
1662 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1675 CGACTATCGT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
38 12 0.26
39 15 0.32
40 3 0.06
41 17 0.36
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (39 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGATAGGAAA
Found at i:2270 original size:32 final size:32
Alignment explanation
Indices: 2209--2288 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
2199 CGAGAATGAA
**
2209 AATCGCAACGCGGAAATGACTATCACAACGAGAG
1 AATCGCAACGC-G-AATGAAAATCACAACGAGAG
* *
2243 AATCGCAACGCGAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAATGAAAATCACAACGAGAG
*
2275 AATCGCAACACGAA
1 AATCGCAACGCGAA
2289 ACCAAAATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 29 0.71
33 1 0.02
34 11 0.27
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.11
Consensus pattern (32 bp):
AATCGCAACGCGAATGAAAATCACAACGAGAG
Found at i:2320 original size:14 final size:14
Alignment explanation
Indices: 2301--2354 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
2291 CAAAATCGCA
2301 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2315 TTGCGATTTTCATTTCGTG
1 TTGCGA--TTC-TCTC--G
2334 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
2348 TTGCGAT
1 TTGCGAT
2355 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 14 0.42
16 6 0.18
17 6 0.18
19 7 0.21
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2343 original size:33 final size:33
Alignment explanation
Indices: 2296--2403 Score: 117
Period size: 33 Copynumber: 3.1 Consensus size: 33
2286 GAAACCAAAA
*
2296 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
* **
2329 TCGTGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
2362 TCCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATT
1 T-CGCGTTGCG------ATTCTCTCGTTGCGATTTTCATT
2402 TC
1 TC
2404 AACCAAAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 30 0.49
34 8 0.13
39 1 0.02
40 22 0.36
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2380 original size:20 final size:21
Alignment explanation
Indices: 2340--2403 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
2330 CGTGTTGCGA
* **
2340 TTCTCTCGTTGCGATAGTCAT
1 TTCTCGCGTTGCGATTTTCAT
2361 TTC-CGCGTTGCGATTTTCA-
1 TTCTCGCGTTGCGATTTTCAT
*
2380 TTCTCTCGTTGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
2401 TTC
1 TTC
2404 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 28 0.76
21 6 0.16
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:4295 original size:90 final size:88
Alignment explanation
Indices: 4092--4321 Score: 326
Period size: 90 Copynumber: 2.6 Consensus size: 88
4082 CTAAACTTTA
4092 TTAACACTGTGAAGTTAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGT--ATATTGGTTGCT
1 TTAACACTGTGAAGTTAGTATTTGTC-TTTGTTTTGTCTTTTGGTTGAAGTAAATATTGGTTGCT
4155 GCCAATTTGCTAAACTGTGTATTCT
65 GCCAATTTGCTAAAC-GTGTATTCT
*
4180 TTAACACTGTGAAGTTAGTATTTGTC-TTGTTTT-TCTTTTGGTTGAAAGTAAATTTATTCGTTT
1 TTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAA--TATT-GGTT
4243 GCTGCCAATTCTGCTAAAC-TGTATTCT
62 GCTGCCAATT-TGCTAAACGTGTATTCT
* * *
4270 TTAATACTCTGAATTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
1 TTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
4322 TGCAATCAAT
Statistics
Matches: 129, Mismatches: 4, Indels: 15
0.87 0.03 0.10
Matches are distributed among these distances:
85 11 0.09
86 11 0.09
88 27 0.21
90 35 0.27
91 26 0.20
92 19 0.15
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (88 bp):
TTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATATTGGTTGCTG
CCAATTTGCTAAACGTGTATTCT
Found at i:4437 original size:20 final size:19
Alignment explanation
Indices: 4410--4509 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
4400 TCTTTTGGTT
*
4410 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
4429 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
4449 GAAACGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4468 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
4487 GAAACCAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4506 GAAA
1 GAAA
4510 CTATAATCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
19 57 0.76
20 18 0.24
ACGTcount: A:0.49, C:0.22, G:0.21, T:0.08
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4578 original size:33 final size:33
Alignment explanation
Indices: 4534--4613 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
4524 GGATTTTTGG
* *
4534 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
* *
4567 TTTCGCATTGCGATTCTCTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
4600 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
4614 AGTCATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:4579 original size:19 final size:18
Alignment explanation
Indices: 4555--4613 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
4545 GATTTTGTCG
4555 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
4573 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
*
4588 TTGTGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
4606 GTTGCGAT
1 -TTGCGAT
4614 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.23
17 7 0.23
19 12 0.39
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:5115 original size:41 final size:42
Alignment explanation
Indices: 5068--5155 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
5058 CCTATCGTTG
* *
5068 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCTCCCACCTTTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGTCCCTCCCACCATTC
* * *
5109 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
5151 AAGAG
1 AAGAG
5156 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 4 0.10
41 16 0.40
42 20 0.50
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:5154 original size:21 final size:21
Alignment explanation
Indices: 5093--5155 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
5083 TTCCTCGAGA
*
5093 GTCCCTCCCACCTTTCAAGAG
1 GTCCCTCCCACCATTCAAGAG
** * * *
5114 G-CCACTGTCATCGTTGAAGAG
1 GTCC-CTCCCACCATTCAAGAG
5135 GTCCCTCCCACCATTCAAGAG
1 GTCCCTCCCACCATTCAAGAG
5156 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
GTCCCTCCCACCATTCAAGAG
Found at i:6518 original size:14 final size:14
Alignment explanation
Indices: 6499--6534 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6489 ATTGTTTAAT
6499 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
6513 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
6527 TGATTTGT
1 TGATTTGT
6535 TTAATTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6688 original size:33 final size:33
Alignment explanation
Indices: 6640--6712 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
6630 CAAAAATGAT
* * * *
6640 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCAAAATGAAAATCGCAACGACAAA
6673 ATCGCAACGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCAAAATGAAAATCGCAACGACAAA
6706 ATCGCAA
1 ATCGCAA
6713 TGCGAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCAAAATGAAAATCGCAACGACAAA
Found at i:6699 original size:19 final size:19
Alignment explanation
Indices: 6640--6707 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
6630 CAAAAATGAT
* *
6640 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCAAAATGAAA
*
6659 ATCGCAACG----A-GAGA
1 ATCGCAACGCAAAATGAAA
6673 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCAAAATGAAA
6692 ATCGCAACGACAAAAT
1 ATCGCAACG-CAAAAT
6708 CGCAATGCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
18 1 0.03
19 20 0.50
20 6 0.15
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCAAAATGAAA
Found at i:6735 original size:18 final size:18
Alignment explanation
Indices: 6704--6743 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6694 CGCAACGACA
* *
6704 AAATCGCAATGCGAAACT
1 AAATCACAACGCGAAACT
6722 AAATCACAACGCGAAACT
1 AAATCACAACGCGAAACT
6740 AAAT
1 AAAT
6744 TCGCGTTGCG
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:0.50, C:0.23, G:0.12, T:0.15
Consensus pattern (18 bp):
AAATCACAACGCGAAACT
Found at i:6765 original size:19 final size:19
Alignment explanation
Indices: 6743--6860 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
6733 CGAAACTAAA
6743 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** *
6762 TTCGTATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
6777 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
*
6795 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
6810 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
6828 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
6847 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
6861 AGACATTAAG
Statistics
Matches: 70, Mismatches: 18, Indels: 21
0.64 0.17 0.19
Matches are distributed among these distances:
14 16 0.23
16 5 0.07
17 5 0.07
19 34 0.49
20 10 0.14
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:6784 original size:33 final size:33
Alignment explanation
Indices: 6747--6840 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
6737 ACTAAATTCG
* *
6747 CGTTGCGATTTTCATTTCGTATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
6780 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
6813 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
6841 AGTCATTTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:6859 original size:20 final size:20
Alignment explanation
Indices: 6813--6906 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
6803 GCGATTCTCT
**
6813 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
6832 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
6852 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
6871 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
6893 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
6907 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:9406 original size:24 final size:24
Alignment explanation
Indices: 9372--9425 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
9362 CTGAAAAATC
9372 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
9396 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
9420 ATCAAA
1 ATCAAA
9426 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:9439 original size:24 final size:24
Alignment explanation
Indices: 9372--9439 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
9362 CTGAAAAATC
* * *
9372 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
9396 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
9420 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
9440 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:10309 original size:20 final size:21
Alignment explanation
Indices: 10286--10654 Score: 313
Period size: 20 Copynumber: 18.3 Consensus size: 21
10276 AGAATCTCGT
10286 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
10306 TGCGA-TTACGTAAATCG-AA
1 TGCGATTTACGTAAATCGCAA
* * * *
10325 GTGCAAATTAGGAAAATCGCAA
1 -TGCGATTTACGTAAATCGCAA
10347 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
10367 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
10387 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
10407 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
10428 TGTGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
10448 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
10469 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
10490 TGCG-GTTACGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAA
10509 TGCGATTTACG---ATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
10527 TGCGA-ATACGT-AACCGCAT
1 TGCGATTTACGTAAATCGCAA
* * * *
10546 TGCGATTTTCCTAATTCGCAT
1 TGCGATTTACGTAAATCGCAA
*
10567 TGCGATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
10587 TGCGATTTACGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* * *
10607 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* *
10628 CGCGAATTTA-GGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
10649 TGCGAT
1 TGCGAT
10655 AGTCAGAATC
Statistics
Matches: 293, Mismatches: 43, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
17 4 0.01
18 10 0.03
19 26 0.09
20 140 0.48
21 107 0.37
22 6 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:10343 original size:41 final size:41
Alignment explanation
Indices: 10297--10653 Score: 324
Period size: 41 Copynumber: 8.8 Consensus size: 41
10287 GCGATTTACT
*
10297 AAATCGCAATGCGATTACGTAAATCG-AAGTGCAAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGA
* *
10338 AAATCGCAATGCGATTACGTAAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
10378 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
*
10419 AAATCGCAATGTGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* * * *
10460 AAATCGCAATGCGAATTAGGAAAATCGCAATGCG-GTTACG-
1 AAATCGCAATGCG-ATTACGTAAATCGCAATGCGAATTAGGA
* * * *
10500 TATTCGCATTGCGATTTACG---ATCGCAATGCGAA-TACG-
1 AAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATTAGGA
* * * * * * * * *
10537 TAACCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACG-
1 AAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATTAGGA
* * * *
10578 TAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGA
1 AAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATTAGGA
* *
10619 AAATCGCAACGCGAATTTA-GGAAATCGCAATGCGA
1 AAATCGCAATGCG-A-TTACGTAAATCGCAATGCGA
10654 TAGTCAGAAT
Statistics
Matches: 270, Mismatches: 34, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
37 31 0.11
39 1 0.00
40 79 0.29
41 123 0.46
42 36 0.13
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
Found at i:10385 original size:81 final size:81
Alignment explanation
Indices: 10286--10492 Score: 310
Period size: 81 Copynumber: 2.5 Consensus size: 81
10276 AGAATCTCGT
10286 TGCGATTTAC-TAAATCGCAATGCGATTACGTAAATCG-AAGTGCAAATTAGGAAAATCGCAATG
1 TGCGA-TTACGTAAATCGCAATGCGATTACGTAAATCGCAA-TGCAAATTAGGAAAATCGCAATG
10349 CGATTACGTAAATCGCAA
64 CGATTACGTAAATCGCAA
* *
10367 TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGTG
1 TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCAAATTAGGAAAATCGCAATGCG
10432 ATTACGTAAATCGCAA
66 ATTACGTAAATCGCAA
* * * *
10448 TGCGAATTAGGAAAATCGCAATGCGAATTAGGAAAATCGCAATGC
1 TGCG-ATTACGTAAATCGCAATGCG-ATTACGTAAATCGCAATGC
10493 GGTTACGTAT
Statistics
Matches: 116, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
80 4 0.03
81 75 0.65
82 20 0.17
83 17 0.15
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (81 bp):
TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCAAATTAGGAAAATCGCAATGCG
ATTACGTAAATCGCAA
Found at i:10632 original size:21 final size:21
Alignment explanation
Indices: 10608--10653 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
10598 TATTCGCATT
10608 GCGAA-TTAGGAAAATCGCAAC
1 GCGAATTTAGG-AAATCGCAAC
*
10629 GCGAATTTAGGAAATCGCAAT
1 GCGAATTTAGGAAATCGCAAC
10650 GCGA
1 GCGA
10654 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTTAGGAAATCGCAAC
Found at i:12065 original size:20 final size:20
Alignment explanation
Indices: 12040--12080 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12030 AGATCTACGT
12040 TGTTTGAGGCATA-TTTTGGG
1 TGTTTG-GGCATAGTTTTGGG
*
12060 TGTTTGGGCTTAGTTTTGGG
1 TGTTTGGGCATAGTTTTGGG
12080 T
1 T
12081 CTAGGGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.10, C:0.05, G:0.37, T:0.49
Consensus pattern (20 bp):
TGTTTGGGCATAGTTTTGGG
Found at i:13386 original size:43 final size:43
Alignment explanation
Indices: 13298--13387 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
13288 TAATCTTTTA
** * * * *
13298 AATCTTATTTTTTATCTTTATAAATGAGGTTTTAATTTTATTC
1 AATCTTACCTTTTATATTTATAAATGAAGTTCTAATTTTACTC
*
13341 AATCTTACCTTTTATATTTATAATTGAAGTCTCTAATTTT-CTC
1 AATCTTACCTTTTATATTTATAAATGAAGT-TCTAATTTTACTC
13384 AATC
1 AATC
13388 CCTTTTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 31 0.79
44 8 0.21
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (43 bp):
AATCTTACCTTTTATATTTATAAATGAAGTTCTAATTTTACTC
Found at i:13559 original size:94 final size:95
Alignment explanation
Indices: 13397--13670 Score: 337
Period size: 94 Copynumber: 2.9 Consensus size: 95
13387 CCCTTTTTTT
*
13397 ACCTTTATAATTGAGGCACCTAATTTTTTAATCTC-GCTTTTTAACTTTATAATT-AAGGC-CTT
1 ACCTTTATAATTGAGGC-CCTAATTTTTTAATCTCAACTTTTTAACTTTATAATTGAA-GCTC-T
13459 TAAGTTTTTTTAATCTCACTTTCTACCATTTCC
63 TAAGTTTTTTTAATCTCACTTTCTACCATTTCC
*
13492 ACCTTTATAATTGA-GCCTCTAATTTTTTAATC-CAACTTTTTAACTTTATAATTGATGCTCTTA
1 ACCTTTATAATTGAGGCC-CTAATTTTTTAATCTCAACTTTTTAACTTTATAATTGAAGCTCTTA
* * *** *
13555 AGTTTTTTCAATATCACTTTCTATGTTTTCT
65 AGTTTTTTTAATCTCACTTTCTACCATTTCC
* * *
13586 ACCTTTACAATTGAGGCCCCTAAGTTTTTTCAATCTCAA-TTTTTACCTTTATAATTGAAGCTCC
1 ACCTTTATAATTGAGG-CCCTAA-TTTTTT-AATCTCAACTTTTTAACTTTATAATTGAAGCTCT
13650 TAA-TTTTTTTAATCTCACTTT
63 TAAGTTTTTTTAATCTCACTTT
13671 TTTAATTTTA
Statistics
Matches: 156, Mismatches: 14, Indels: 17
0.83 0.07 0.09
Matches are distributed among these distances:
93 2 0.01
94 77 0.49
95 21 0.13
96 24 0.15
97 29 0.19
98 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (95 bp):
ACCTTTATAATTGAGGCCCTAATTTTTTAATCTCAACTTTTTAACTTTATAATTGAAGCTCTTAA
GTTTTTTTAATCTCACTTTCTACCATTTCC
Found at i:13747 original size:88 final size:86
Alignment explanation
Indices: 13589--13817 Score: 273
Period size: 88 Copynumber: 2.6 Consensus size: 86
13579 GTTTTCTACC
* * * *
13589 TTTACAATTGAGGCCCCTAAGTTTTTTCAATCTCAATTTTTACCTTTATAATTGAAGCTCCTAA-
1 TTTATAATTGA-GACCCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAAGCTCATAAG
* * *
13653 TTTTTTTAATCTC-ACTTTTTTAAT
65 GTTTTTCAATCTCGA---TTATAAT
* *
13677 TTTATAATTGAGACCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGGTTCATAAG
1 TTTATAATTGAGACCC-TAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAAGCTCATAAG
*
13742 GTTTTTCAATCTCGATTATACT
65 GTTTTTCAATCTCGATTATAAT
13764 TTTATAATTGAGACCCTAAGTTTTTTTTTTCAATCTCAATTTCTACCTTTATAA
1 TTTATAATTGAGACCCTAAG----TTTTTTCAATCTCAATTTCTACCTTTATAA
13818 GTAAGGCCTC
Statistics
Matches: 124, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
86 4 0.03
87 25 0.20
88 53 0.43
89 11 0.09
90 31 0.25
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (86 bp):
TTTATAATTGAGACCCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAAGCTCATAAGG
TTTTTCAATCTCGATTATAAT
Found at i:13790 original size:43 final size:43
Alignment explanation
Indices: 13580--13841 Score: 224
Period size: 44 Copynumber: 5.9 Consensus size: 43
13570 ACTTTCTATG
* *
13580 TTTTCTACCTTTACAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
1 TTTT-TACCTTTATAATTGA-GACCCTAAGTTTTTTCAATCTCAA
* *
13625 TTTTTACCTTTATAATTGA-AGCTCCTAA-TTTTTTTAATCTCACT
1 TTTTTACCTTTATAATTGAGA-C-CCTAAGTTTTTTCAATCTCA-A
**
13669 TTTTTAATTTTATAATTGAGACCCTTAAGTTTTTTCAATCTCAA
1 TTTTTACCTTTATAATTGAGACCC-TAAGTTTTTTCAATCTCAA
* ** * * *
13713 TTTCTACCTTTATAATTGAGGTTCATAAGGTTTTTCAATCTCGA
1 TTTTTACCTTTATAATTGA-GACCCTAAGTTTTTTCAATCTCAA
* *
13757 -TTATACTTTTATAATTGAGACCCTAAGTTTTTTTTTTCAATCTCAA
1 TTTTTACCTTTATAATTGAGACCCTAAG----TTTTTTCAATCTCAA
* * * * *
13803 TTTCTACCTTTATAAGTAAGGCCTCTAACTTTTTTCAAT
1 TTTTTACCTTTATAATTGAGACC-CTAAGTTTTTTCAAT
13842 TTCATAAAAT
Statistics
Matches: 175, Mismatches: 29, Indels: 27
0.76 0.13 0.12
Matches are distributed among these distances:
42 6 0.03
43 32 0.18
44 83 0.47
45 20 0.11
46 13 0.07
47 17 0.10
48 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (43 bp):
TTTTTACCTTTATAATTGAGACCCTAAGTTTTTTCAATCTCAA
Found at i:13837 original size:90 final size:85
Alignment explanation
Indices: 13589--13846 Score: 270
Period size: 88 Copynumber: 2.9 Consensus size: 85
13579 GTTTTCTACC
* * * *
13589 TTTACAATTGAGGCCCCTAAGTTTTTTCAATCTCAATTTTTACCTTTATAATTGAA-GCTCCTAA
1 TTTATAATTGAGACCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATT-AAGGCT-CTAA
* *
13653 TTTTTTTAATCTCACTTTTTTAAT
64 TTTTTTCAATCTCA--TTTATAAT
* *
13677 TTTATAATTGAGACCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGGTTCATAAG
1 TTTATAATTGAGACCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGGCTC-TAA-
* *
13742 GTTTTTCAATCTCGA-TTATACT
64 TTTTTTCAATCTC-ATTTATAAT
*
13764 TTTATAATTGAGACCC-TAAGTTTTTTTTTTCAATCTCAATTTCTACCTTTATAAGTAAGGCCTC
1 TTTATAATTGAGACCCTTAAG----TTTTTTCAATCTCAATTTCTACCTTTATAATTAAGG-CTC
*
13828 TAACTTTTTTCAATTTCAT
61 TAA-TTTTTTCAATCTCAT
13847 AAAATTTACG
Statistics
Matches: 144, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
86 4 0.03
87 23 0.16
88 54 0.38
89 12 0.08
90 49 0.34
91 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (85 bp):
TTTATAATTGAGACCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGGCTCTAATT
TTTTCAATCTCATTTATAAT
Found at i:15135 original size:17 final size:17
Alignment explanation
Indices: 15115--15149 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15105 GAATATTTTT
15115 TTTATTTGGG-TTTAAAA
1 TTTA-TTGGGTTTTAAAA
15132 TTTATTGGGTTTTAAAA
1 TTTATTGGGTTTTAAAA
15149 T
1 T
15150 ATTAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTATTGGGTTTTAAAA
Found at i:15141 original size:16 final size:16
Alignment explanation
Indices: 15115--15163 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
15105 GAATATTTTT
15115 TTTATTTGGGTTTAAAA
1 TTTA-TTGGGTTTAAAA
15132 TTTATTGGGTTTTAAAA
1 TTTATTGGG-TTTAAAA
* *
15149 TATTAATGAGTTTAA
1 T-TTATTGGGTTTAA
15164 GGTTAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.18
17 17 0.61
18 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (16 bp):
TTTATTGGGTTTAAAA
Found at i:18500 original size:13 final size:13
Alignment explanation
Indices: 18493--18533 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
18483 TCTTTTCTTC
18493 TTAACTTTTCACT
1 TTAACTTTTCACT
18506 TTAACTTTTCACACT
1 TTAACTTTT--CACT
18521 TTAACTTTTCACT
1 TTAACTTTTCACT
18534 CTTCCCCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAACTTTTCACT
Found at i:18522 original size:15 final size:15
Alignment explanation
Indices: 18493--18532 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
18483 TCTTTTCTTC
18493 TTAACTTTT--CACT
1 TTAACTTTTCACACT
18506 TTAACTTTTCACACT
1 TTAACTTTTCACACT
18521 TTAACTTTTCAC
1 TTAACTTTTCAC
18533 TCTTCCCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 9 0.36
15 16 0.64
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAACTTTTCACACT
Found at i:34970 original size:17 final size:15
Alignment explanation
Indices: 34948--34982 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
34938 TTTATAAAAA
34948 AAATTTATAAATTTTAT
1 AAATTTA-AAATTTT-T
34965 AAATTTAAAATTTTT
1 AAATTTAAAATTTTT
34980 AAA
1 AAA
34983 AAATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 7 0.39
17 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTAAAATTTTT
Found at i:38046 original size:21 final size:23
Alignment explanation
Indices: 38017--38074 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
38007 ATATCAAATT
*
38017 ATATGAAAAAATTAAT-AAAA-A
1 ATATTAAAAAATTAATGAAAACA
38038 ATATTAAAAAA-T-ATGAAAACA
1 ATATTAAAAAATTAATGAAAACA
38059 AT-TTACAAAAATTAAT
1 ATATTA-AAAAATTAAT
38075 CCTAAATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.06
20 8 0.26
21 18 0.58
22 1 0.03
23 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (23 bp):
ATATTAAAAAATTAATGAAAACA
Found at i:41178 original size:12 final size:12
Alignment explanation
Indices: 41135--41180 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
41125 CGTTGGACAC
41135 GGGTCGGGTCTT-
1 GGGTCGGGT-TTG
41147 -GGTCGGGTTTG
1 GGGTCGGGTTTG
* *
41158 GGTTTGGGTTTG
1 GGGTCGGGTTTG
41170 GGGTCGGGTTT
1 GGGTCGGGTTT
41181 TGTTATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 8 0.29
12 18 0.64
ACGTcount: A:0.00, C:0.09, G:0.52, T:0.39
Consensus pattern (12 bp):
GGGTCGGGTTTG
Found at i:41737 original size:42 final size:42
Alignment explanation
Indices: 41672--41771 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
41662 TGGATGACCC
* * *
41672 GAAGGTCTTA-TCATCTTGGTCGAAAGACTTA-TAAATGGCCT
1 GAAGGACTTACTCATCATGCTCGAAAGACTTACT-AATGGCCT
* * *
41713 GAATGACTTACTCATCATGCTCGAAAGACTTACTGATGGCTT
1 GAAGGACTTACTCATCATGCTCGAAAGACTTACTAATGGCCT
*
41755 GAAGGAATTACTCATCA
1 GAAGGACTTACTCATCA
41772 AAAAACCCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 8 0.16
42 40 0.82
43 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
GAAGGACTTACTCATCATGCTCGAAAGACTTACTAATGGCCT
Found at i:42161 original size:276 final size:275
Alignment explanation
Indices: 41635--42197 Score: 808
Period size: 276 Copynumber: 2.0 Consensus size: 275
41625 ACCGAAAATG
* *
41635 TTGAAAACATCGTGCCCGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGGTCGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGGTCGAAAGAC
* * ** * * **
41700 TTATAAATGGCCTGAATGACTTACTCATCATGCTCGAAAGACTTACTGATGGCTTGAAGGAATTA
66 TTATAAATGACCTGAAGGACTTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAAGGAATTA
41765 CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTTCCAAGGAACCCCTAAAAATTAG
131 CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTTCCAAGGAACCCCTAAAAATTAG
* *
41830 TCTTAGCTTCCTTTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATC-AGACTT
196 GCTTAGCTT-CTCTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATCAAG-CTT
41894 AGTTTCTAAAAACTCAT
259 AGTTTCTAAAAACTCAT
* * *
41911 TTGAGAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGTTCGAAAGAC
1 TTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGGTCGAAAGAC
* * * * *
41976 TTATAGATGACCTGGAGGATTTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAATGACTTA
66 TTATAAATGACCTGAAGGACTTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAAGGAATTA
* *
42041 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATTAAGGAACCCCTAAAAAT
131 CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTT-TC--CAAGGAACCCCTAAAAAT
* * * * *
42106 TAGGCTTAGCTT-TCTTGAAAATTCTTTGGAGATAATCATTAAGAAATCC-CTGAAAATCAAGCT
193 TAGGCTTAGCTTCTCTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATCAAGCT
*
42169 TAGTTTTTAAAAACTCAT
258 TAGTTTCTAAAAACTCAT
42187 TTGAAAACATC
1 TTGAAAACATC
42198 AAGAAACCCT
Statistics
Matches: 254, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
276 191 0.75
277 35 0.14
279 28 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (275 bp):
TTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGGTCGAAAGAC
TTATAAATGACCTGAAGGACTTAAGCATCATGCTCAAAAGACTAACTGATGGCCCGAAGGAATTA
CTCATCAAAAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTTCCAAGGAACCCCTAAAAATTAG
GCTTAGCTTCTCTTAAAAACTCTTTGGAGATAATCATAAAAAAAACCTCTGAAAATCAAGCTTAG
TTTCTAAAAACTCAT
Found at i:42162 original size:57 final size:53
Alignment explanation
Indices: 42084--42225 Score: 146
Period size: 57 Copynumber: 2.6 Consensus size: 53
42074 TTCTTAGTTG
* * *
42084 TCATTAAGGAACCCCTAAAAATTAGGCTTAGCTTTCTTGAAAATTC-TTTGGAGATAA
1 TCATTAA-GAAACCCTAAAAATTAGGCTTAGCTTT-TTAAAAACTCATTT-GA-A-AA
* * *
42141 TCATTAAGAAATCCCTGAAAATCAAGCTTAG-TTTTTAAAAACTCATTTGAAAA
1 TCATTAAGAAA-CCCTAAAAATTAGGCTTAGCTTTTTAAAAACTCATTTGAAAA
*
42194 -CATCAAGAAACCCTAAAAATTAGGCTTAGCTT
1 TCATTAAGAAACCCTAAAAATTAGGCTTAGCTT
42226 CTTATTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
51 16 0.22
52 11 0.15
53 2 0.03
54 1 0.01
55 10 0.14
56 9 0.12
57 23 0.32
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (53 bp):
TCATTAAGAAACCCTAAAAATTAGGCTTAGCTTTTTAAAAACTCATTTGAAAA
Found at i:43407 original size:1 final size:1
Alignment explanation
Indices: 43401--43457 Score: 69
Period size: 1 Copynumber: 57.0 Consensus size: 1
43391 TCCTTTTCTC
* * * * *
43401 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTATTTTTTTTCTTTTTTTATGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43458 CTATATCTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.04, C:0.04, G:0.02, T:0.91
Consensus pattern (1 bp):
T
Found at i:43408 original size:11 final size:10
Alignment explanation
Indices: 43372--43457 Score: 84
Period size: 10 Copynumber: 8.1 Consensus size: 10
43362 TTATTTCTTC
43372 TTTCTTTCTTT
1 TTTCTTT-TTT
43383 CTTTCTTTTCCTT
1 -TTTCTTTT--TT
43396 TTCTCTTTTTT
1 TT-TCTTTTTT
43407 TTT-TTTTTT
1 TTTCTTTTTT
*
43416 TTTTTTTTTT
1 TTTCTTTTTT
43426 TTTCTATTTTT
1 TTTCT-TTTTT
43437 TTTCTTTTTT
1 TTTCTTTTTT
* *
43447 TATGTTTTTT
1 TTTCTTTTTT
43457 T
1 T
43458 CTATATCTCT
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
9 9 0.14
10 25 0.38
11 15 0.23
12 9 0.14
13 8 0.12
ACGTcount: A:0.02, C:0.12, G:0.01, T:0.85
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:43436 original size:31 final size:31
Alignment explanation
Indices: 43394--43457 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
43384 TTTCTTTTCC
* * * *
43394 TTTTCTCTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTCTATTTTTTTTCTTTTTTTATGTTTTT
43425 TTTTCTATTTTTTTTCTTTTTTTATGTTTTT
1 TTTTCTATTTTTTTTCTTTTTTTATGTTTTT
43456 TT
1 TT
43458 CTATATCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.03, C:0.06, G:0.02, T:0.89
Consensus pattern (31 bp):
TTTTCTATTTTTTTTCTTTTTTTATGTTTTT
Found at i:43444 original size:8 final size:8
Alignment explanation
Indices: 43372--43447 Score: 68
Period size: 8 Copynumber: 9.4 Consensus size: 8
43362 TTATTTCTTC
*
43372 TTTCTTTC
1 TTTCTTTT
43380 TTTCTTTCT
1 TTTCTTT-T
*
43389 TTTCCTTT
1 TTTCTTTT
*
43397 TCTCTTTT
1 TTTCTTTT
43405 TTT-TTTT
1 TTTCTTTT
43412 TTT-TTTT
1 TTTCTTTT
43419 TTT-TTTT
1 TTTCTTTT
43426 TTTCTATTTTT
1 TTTC---TTTT
43437 TTTCTTTT
1 TTTCTTTT
43445 TTT
1 TTT
43448 ATGTTTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
7 21 0.36
8 23 0.40
9 6 0.10
11 8 0.14
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTCTTTT
Found at i:43454 original size:29 final size:29
Alignment explanation
Indices: 43394--43461 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
43384 TTTCTTTTCC
* * * * *
43394 TTTTCTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTCTATTTTTTTTCTTTTTTTATGT
43423 TTTTTTCTATTTTTTTTCTTTTTTTATGT
1 TTTTTTCTATTTTTTTTCTTTTTTTATGT
43452 TTTTTTCTAT
1 TTTTTTCTAT
43462 ATCTCTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.04, C:0.07, G:0.01, T:0.87
Consensus pattern (29 bp):
TTTTTTCTATTTTTTTTCTTTTTTTATGT
Found at i:43459 original size:18 final size:16
Alignment explanation
Indices: 43401--43457 Score: 80
Period size: 15 Copynumber: 3.5 Consensus size: 16
43391 TCCTTTTCTC
43401 TTTTTTTTTTTTTTT-
1 TTTTTTTTTTTTTTTA
*
43416 TTTTTTTTTTTTTCTA
1 TTTTTTTTTTTTTTTA
43432 TTTTTTTTCTTTTTTTA
1 TTTTTTTT-TTTTTTTA
43449 TGTTTTTTT
1 T-TTTTTTT
43458 CTATATCTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 14 0.38
16 8 0.22
17 8 0.22
18 7 0.19
ACGTcount: A:0.04, C:0.04, G:0.02, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTA
Found at i:43470 original size:29 final size:29
Alignment explanation
Indices: 43412--43471 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
43402 TTTTTTTTTT
* * * * *
43412 TTTTTTTTTTTTTTTTTCTATTTTTTTTC
1 TTTTTTTATGTTTTTTTCTATATCTCTTC
43441 TTTTTTTATGTTTTTTTCTATATCTCTTC
1 TTTTTTTATGTTTTTTTCTATATCTCTTC
43470 TT
1 TT
43472 CTTTCTCTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.82
Consensus pattern (29 bp):
TTTTTTTATGTTTTTTTCTATATCTCTTC
Found at i:46540 original size:44 final size:44
Alignment explanation
Indices: 46474--46721 Score: 345
Period size: 44 Copynumber: 5.6 Consensus size: 44
46464 CAAGATGGCA
* * *
46474 ATGTGCAAGGGTAAGTCTTTACCGTTACCGTAGGCTCTTCTACT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
*
46518 ATGTGCAAGGGTAAGTCGTTACCGTTACCGTAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
*
46562 ATGTGCAAGGGTAAGTCCTTACCATTACCGTAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
* * * **
46606 ACGTGCAAGGTTAAGTCCTTATCGTTACCACAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
* * *
46650 ACGTGCAAGTGTAAGTTCTTACCGTTACCGTAGGCTCCTCTGCT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
* *
46694 ATGTGTC-AGTGTAAATCCTTACCGTTAC
1 ATGTG-CAAGGGTAAGTCCTTACCGTTAC
46722 TACTGACTCC
Statistics
Matches: 183, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
44 182 0.99
45 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (44 bp):
ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCT
Found at i:46590 original size:88 final size:88
Alignment explanation
Indices: 46474--46762 Score: 346
Period size: 88 Copynumber: 3.3 Consensus size: 88
46464 CAAGATGGCA
* * * *
46474 ATGTGCAAGGGTAAGTCTTTACCGTTACCGTAGGCTCTTCTACTATGTGCAAGGGTAAGTCGTTA
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTA
**
46539 CCGTTACCGTAGGCTCCTCTGCT
66 CCGTTACCACAGGCTCCTCTGCT
* * *
46562 ATGTGCAAGGGTAAGTCCTTACCATTACCGTAGGCTCCTCTGCTACGTGCAAGGTTAAGTCCTTA
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTA
*
46627 TCGTTACCACAGGCTCCTCTGCT
66 CCGTTACCACAGGCTCCTCTGCT
* * * * *
46650 ACGTGCAAGTGTAAGTTCTTACCGTTACCGTAGGCTCCTCTGCTATGTGTC-AGTGTAAATCCTT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTG-CAAGGGTAAGTCCTT
* * * *
46714 ACCGTTACTACTGACTCCTCTACT
65 ACCGTTACCACAGGCTCCTCTGCT
* ** *
46738 TTGTGCACAGAATAAGACCTTACCG
1 ATGTGCA-AGGGTAAGTCCTTACCG
46763 CAGGTTCCTC
Statistics
Matches: 170, Mismatches: 29, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
88 156 0.92
89 14 0.08
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (88 bp):
ATGTGCAAGGGTAAGTCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTA
CCGTTACCACAGGCTCCTCTGCT
Found at i:46744 original size:132 final size:132
Alignment explanation
Indices: 46474--46762 Score: 334
Period size: 132 Copynumber: 2.2 Consensus size: 132
46464 CAAGATGGCA
* ** * *
46474 ATGTGCAAGGGTAAGTCTTTACCGTTACCGTAGGCTCTTCTACTATGTGCAAGGGTAAGTCGTTA
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCACAGGCTCCTCTACTACGTGCAAGGGTAAGTCGTTA
* * *
46539 CCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCATTACCGTAGGCTCCTCTG
66 CCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAATCCTTACCATTACCGTAGACTCCTCTA
46604 CT
131 CT
* * * * *
46606 ACGTGCAAGGTTAAGTCCTTATCGTTACCACAGGCTCCTCTGCTACGTGCAAGTGTAAGTTC-TT
1 ATGTGCAAGGGTAAGTCCTTACCGTTACCACAGGCTCCTCTACTACGTGCAAGGGTAAG-TCGTT
* *
46670 ACCGTTACCGTAGGCTCCTCTGCTATGTGTC-AGTGTAAATCCTTACCGTTA-C-TACTGACTCC
65 ACCGTTACCGTAGGCTCCTCTGCTATGTG-CAAGGGTAAATCCTTACCATTACCGTA--GACTCC
46732 TCTACT
127 TCTACT
* ** *
46738 TTGTGCACAGAATAAGACCTTACCG
1 ATGTGCA-AGGGTAAGTCCTTACCG
46763 CAGGTTCCTC
Statistics
Matches: 131, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
130 2 0.02
131 1 0.01
132 112 0.85
133 16 0.12
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (132 bp):
ATGTGCAAGGGTAAGTCCTTACCGTTACCACAGGCTCCTCTACTACGTGCAAGGGTAAGTCGTTA
CCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAATCCTTACCATTACCGTAGACTCCTCTA
CT
Found at i:50491 original size:21 final size:19
Alignment explanation
Indices: 50457--50499 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
50447 GAGAATTCAC
50457 TTTGATTTAATTCACGATTCT
1 TTTGATTTAATTCA--ATTCT
**
50478 TTTGATTTCTTTCAATTCT
1 TTTGATTTAATTCAATTCT
50497 TTT
1 TTT
50500 ATTATTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTGATTTAATTCAATTCT
Found at i:51981 original size:21 final size:21
Alignment explanation
Indices: 51957--52001 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
51947 ATCAATTCCT
*
51957 TTTTTGCATTTACAT-TTTGCA
1 TTTTT-CATTCACATCTTTGCA
*
51978 TTTTTCATTCCCATCTTTGCA
1 TTTTTCATTCACATCTTTGCA
51999 TTT
1 TTT
52002 GCATGTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTTCATTCACATCTTTGCA
Found at i:53412 original size:16 final size:16
Alignment explanation
Indices: 53385--53476 Score: 73
Period size: 17 Copynumber: 5.4 Consensus size: 16
53375 AGAATGCAAG
53385 GAAAAGAAAGAGAAAGA
1 GAAAA-AAAGAGAAAGA
53402 GAAAAAAAGAGTAAAAGA
1 GAAAAAAAGAG--AAAGA
53420 GGAAAAAGAA-A-AAAGA
1 -GAAAAA-AAGAGAAAGA
*
53436 G-AAAAAAGAAGAAAAAA
1 GAAAAAAAG-AG-AAAGA
*
53453 GAAAAAGAAGAGAAAAA
1 GAAAAA-AAGAGAAAGA
53470 GAAAAAA
1 GAAAAAA
53477 GAAGAAAAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 21
0.74 0.01 0.24
Matches are distributed among these distances:
13 2 0.03
14 4 0.06
15 2 0.03
16 12 0.19
17 21 0.33
18 11 0.17
19 10 0.16
20 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (16 bp):
GAAAAAAAGAGAAAGA
Found at i:53426 original size:9 final size:8
Alignment explanation
Indices: 53391--53487 Score: 90
Period size: 9 Copynumber: 11.6 Consensus size: 8
53381 CAAGGAAAAG
53391 AAAGAGAA
1 AAAGAGAA
* *
53399 AGAGAAAA
1 AAAGAGAA
*
53407 AAAGAGTA
1 AAAGAGAA
53415 AAAGAGGAA
1 AAAGA-GAA
53424 AAAGA-AA
1 AAAGAGAA
53431 AAAGAGAAA
1 AAAGAG-AA
53440 AAAGAAGAAA
1 AAAG-AG-AA
*
53450 AAAGAAAA
1 AAAGAGAA
53458 AGAAGAGAA
1 A-AAGAGAA
53467 AAAGA-AA
1 AAAGAGAA
53474 AAAGAAGAA
1 AAAG-AGAA
53483 AAAGA
1 AAAGA
53488 AGAAGAAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
7 13 0.18
8 25 0.34
9 27 0.36
10 9 0.12
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (8 bp):
AAAGAGAA
Found at i:53434 original size:7 final size:7
Alignment explanation
Indices: 53422--53484 Score: 58
Period size: 7 Copynumber: 8.7 Consensus size: 7
53412 GTAAAAGAGG
53422 AAAAAGA
1 AAAAAGA
53429 AAAAAG-
1 AAAAAGA
*
53435 AGAAA-A
1 AAAAAGA
*
53441 AAGAAGA
1 AAAAAGA
53448 AAAAAGAA
1 AAAAAG-A
53456 AAAGAAGA
1 AAA-AAGA
53464 GAAAAAGA
1 -AAAAAGA
53472 AAAAAGA
1 AAAAAGA
53479 AGAAAA
1 A-AAAA
53485 AGAAGAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
6 7 0.15
7 20 0.43
8 13 0.28
9 6 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:53482 original size:16 final size:16
Alignment explanation
Indices: 53391--53488 Score: 87
Period size: 16 Copynumber: 5.9 Consensus size: 16
53381 CAAGGAAAAG
*
53391 AAAG-AGAAAGAGAAA
1 AAAGAAGAAAAAGAAA
*
53406 AAA-AGAGTAAAAGAGGAA
1 AAAGA-AG-AAAA-AGAAA
53424 AAAGAA-AAAAGAGAAA
1 AAAGAAGAAAA-AGAAA
53440 AAAGAAGAAAAA-AGAA
1 AAAGAAGAAAAAGA-AA
53456 AAAGAAGAGAAAAAGAAA
1 AAAG-A-AGAAAAAGAAA
53474 AAAGAAGAAAAAGAA
1 AAAGAAGAAAAAGAA
53489 GAAGAAAATA
Statistics
Matches: 70, Mismatches: 3, Indels: 19
0.76 0.03 0.21
Matches are distributed among these distances:
15 4 0.06
16 34 0.49
17 9 0.13
18 21 0.30
19 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (16 bp):
AAAGAAGAAAAAGAAA
Found at i:54150 original size:28 final size:28
Alignment explanation
Indices: 54110--54176 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
54100 GAAGCCAACA
*
54110 TGAAACACATTACCTCCCTAAATTAACC
1 TGAAACACATTACCTCCCCAAATTAACC
*
54138 TGAAACACATTACTTCCCCAAATTAACC
1 TGAAACACATTACCTCCCCAAATTAACC
*
54166 TAAAACACATT
1 TGAAACACATT
54177 GCATTCCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.42, C:0.30, G:0.03, T:0.25
Consensus pattern (28 bp):
TGAAACACATTACCTCCCCAAATTAACC
Found at i:54185 original size:28 final size:27
Alignment explanation
Indices: 54112--54186 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
54102 AGCCAACATG
* *
54112 AAACACATTACCTCCCTAAATTAACCTG
1 AAACACATTACTTCCC-AAATTAACCTA
54140 AAACACATTACTTCCCCAAATTAACCTA
1 AAACACATTACTT-CCCAAATTAACCTA
*
54168 AAACACATTGCATTCCCAA
1 AAACACATTAC-TTCCCAA
54187 GACATCCTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 37 0.88
29 5 0.12
ACGTcount: A:0.41, C:0.32, G:0.03, T:0.24
Consensus pattern (27 bp):
AAACACATTACTTCCCAAATTAACCTA
Found at i:55552 original size:55 final size:54
Alignment explanation
Indices: 55472--55594 Score: 140
Period size: 55 Copynumber: 2.3 Consensus size: 54
55462 GATAATGTTT
* * * ** *
55472 TTTTAAAGAAAATAAGTCCGATTTTTGGAACTTTCTTAATTATTTTTAAATGAGC
1 TTTTAAAGAAACTAAGTACGATTTTTAGAACTTT-TTAACAATTTTCAAATGAGC
* * * *
55527 TTTTAAAGAAACTAAGTATGCTTTTTAGAAGTTTTTGACAATTTTCAAATGAGC
1 TTTTAAAGAAACTAAGTACGATTTTTAGAACTTTTTAACAATTTTCAAATGAGC
55581 -TTTAAAGAAACTAA
1 TTTTAAAGAAACTAA
55595 CTCTTATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 14 0.24
54 16 0.28
55 28 0.48
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (54 bp):
TTTTAAAGAAACTAAGTACGATTTTTAGAACTTTTTAACAATTTTCAAATGAGC
Found at i:55610 original size:53 final size:55
Alignment explanation
Indices: 55513--55618 Score: 144
Period size: 53 Copynumber: 2.0 Consensus size: 55
55503 TTTCTTAATT
* * * *
55513 ATTTTTAAATGAGCTTTTAAAGAAACTAAGTATGCTTTTTAGAAGTTT-TTGACA
1 ATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAGTTTCTTGACA
* *
55567 ATTTTCAAATGAGC-TTTAAAGAAACTAACTCTTATTTTCAGAAGTTTCTTGA
1 ATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAGTTTCTTGA
55619 TATTTTTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 28 0.62
54 17 0.38
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (55 bp):
ATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAGTTTCTTGACA
Found at i:55624 original size:53 final size:55
Alignment explanation
Indices: 55503--55624 Score: 142
Period size: 53 Copynumber: 2.3 Consensus size: 55
55493 TTTTTGGAAC
* * * * * *
55503 TTTCTTAATTATTTTTAAATGAGCTTTTAAAGAAACTAAGTATGCTTTTTAGAAG
1 TTTCTTGACTATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAG
* * *
55558 TTT-TTGACAATTTTCAAATGAGC-TTTAAAGAAACTAACTCTTATTTTCAGAAG
1 TTTCTTGACTATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAG
55611 TTTCTTGA-TATTTT
1 TTTCTTGACTATTTT
55625 TTAAACGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
53 33 0.59
54 20 0.36
55 3 0.05
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (55 bp):
TTTCTTGACTATTTTCAAATGAGCTTTTAAAGAAACTAACTATGATTTTCAGAAG
Found at i:55924 original size:41 final size:42
Alignment explanation
Indices: 55846--55942 Score: 178
Period size: 41 Copynumber: 2.3 Consensus size: 42
55836 GAGCCATCAG
55846 TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
1 TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
*
55888 TAAGTCTTTCGAGCGTGA-GCTTAAATCCTTCGAGTCATCTA
1 TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
55929 TAAGTCTTTCGAGC
1 TAAGTCTTTCGAGC
55943 AAGATGATAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 36 0.67
42 18 0.33
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (42 bp):
TAAGTCTTTCGAGCGTGATGCTTAAATCCTTCAAGTCATCTA
Found at i:55941 original size:20 final size:20
Alignment explanation
Indices: 55879--55941 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
55869 AAATCCTTCA
55879 AGTCATCTATAAGTCTTTCG
1 AGTCATCTATAAGTCTTTCG
* * * *
55899 AGCGTGAGCT-TAAATCCTTCG
1 A--GTCATCTATAAGTCTTTCG
55920 AGTCATCTATAAGTCTTTCG
1 AGTCATCTATAAGTCTTTCG
55940 AG
1 AG
55942 CAAGATGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 5 0.16
20 12 0.38
21 10 0.31
22 5 0.16
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (20 bp):
AGTCATCTATAAGTCTTTCG
Found at i:56261 original size:144 final size:140
Alignment explanation
Indices: 55950--56312 Score: 485
Period size: 141 Copynumber: 2.6 Consensus size: 140
55940 AGCAAGATGA
* *
55950 TAAGTCTTTCAGGCCATCCATAAGACCTTCGGGCAGGTTGTTTTCAGCATTTCCTTTTCTCGATT
1 TAAGTCTTTCAGGCCATCCATAAGACCTTC-GGCAGGATGTTTTCAACATTTCCTTTTCTCGATT
** * *
56015 CACAACACTTCGAATCAGCAACGCCTTACCAGAGGGGACATTTCCTTTTGCTCGATTCACACACT
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGAACATTTCCTATTGCTCGATTCACACACT
56080 TCGAATCAGCT
130 TCGAATCAGCT
* ** * * *
56091 TAAGTCTTTCGGGCCATCCATAAGACCTTCAGTAATGATGTTTTCAACATTTACTTTTCTCAATT
1 TAAGTCTTTCAGGCCATCCATAAGACCTTC-GGCAGGATGTTTTCAACATTTCCTTTTCTCGATT
* * *
56156 CACAACACTTCGTATCAGTAATGCCCCACCAGAGAGGTTAACATTTCCTATTGCTCGATTCACAC
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAG-GG--AACATTTCCTATTGCTCGATTCACAC
*
56221 ACTTTGAATCAGCT
127 ACTTCGAATCAGCT
* * * * *
56235 TAAGTCCTTCAGGCCATTCATAAGACCTTCGGCAGGGTGTTTTCAACATTTCCTTTGCCCGATTC
1 TAAGTCTTTCAGGCCATCCATAAGACCTTCGGCAGGATGTTTTCAACATTTCCTTTTCTCGATTC
56300 AC-ACACTTCGAAT
66 ACAACACTTCGAAT
56313 TGGCTTAAGT
Statistics
Matches: 190, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
141 85 0.45
142 12 0.06
143 29 0.15
144 64 0.34
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.32
Consensus pattern (140 bp):
TAAGTCTTTCAGGCCATCCATAAGACCTTCGGCAGGATGTTTTCAACATTTCCTTTTCTCGATTC
ACAACACTTCGAATCAGCAACGCCCCACCAGAGGGAACATTTCCTATTGCTCGATTCACACACTT
CGAATCAGCT
Found at i:56340 original size:83 final size:84
Alignment explanation
Indices: 56195--56407 Score: 295
Period size: 83 Copynumber: 2.5 Consensus size: 84
56185 CAGAGAGGTT
* ** *
56195 AACATTTCCTATTGCTCGATTCACACACTTTGAATCAGCTTAAGTCCTTCAGGCCATTCATAAGA
1 AACATTTCCT-TTGCTCGATTCACACACTTCGAATCAGCTTAAGTAATTCAGGCCATCCATAAGA
*
56260 CCTTC-GGCAGGGTGTTTTC
65 CCTTCGGGCAGGATGTTTTC
* **
56279 AACATTTCCTTTGCCCGATTCACACACTTCGAATTGGCTTAAGTAATTC-GAGCCATCCATAAGA
1 AACATTTCCTTTGCTCGATTCACACACTTCGAATCAGCTTAAGTAATTCAG-GCCATCCATAAGA
56343 CCTTCGGGCAGGATGTTTTC
65 CCTTCGGGCAGGATGTTTTC
* *
56363 AACATTTCCTCTGCTCGATTCACAACACTTCGAATCAGCATAAGT
1 AACATTTCCTTTGCTCGATTCAC-ACACTTCGAATCAGCTTAAGT
56408 CAGTTGGGCC
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 50 0.44
84 44 0.39
85 18 0.16
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (84 bp):
AACATTTCCTTTGCTCGATTCACACACTTCGAATCAGCTTAAGTAATTCAGGCCATCCATAAGAC
CTTCGGGCAGGATGTTTTC
Found at i:57820 original size:136 final size:136
Alignment explanation
Indices: 57524--57847 Score: 341
Period size: 136 Copynumber: 2.4 Consensus size: 136
57514 ATGGTAAACC
* * **
57524 AATCAACATTTCAAATAGAGAGTTTATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCA
1 AATCAACATTTCACATAGAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGGAGAAAAAGTTCA
* *
57589 TAATGAGAAGAACTTGTTCAACCTTCGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCT
66 TAATAAGAAGAACTTGTTCAACCTTCACTCGATTAATCACATAT---GTTGAATCAGCAACACCT
57654 CGCTTGAGG
128 CGCTTGAGG
* * * *
57663 AATCAACATTTC-CAATGGAGAGTTCATAATGTGAATAACTCAT-TCGAAAAAGGGAGAAGAAGT
1 AATCAACATTTCAC-ATAGAGAGTTCATAATGAGAAGAACTCATCT-G-AAAAGGGAGAAAAAGT
* * * * ** ** *
57726 TCATAATAAGAAGAGCTTGTTCGACCTATCACTTGATTCATGGCAT-T-TTGAATCAGTGACGCC
63 TCATAATAAGAAGAACTTGTTCAACCT-TCACTCGATTAATCACATATGTTGAATCAGCAACACC
57789 TCGCTTGAGG
127 TCGCTTGAGG
* * * * *
57799 GATCAATATTTCACATAGAGAGTTCATAATCAGAAGATCTCATCCGAAA
1 AATCAACATTTCACATAGAGAGTTCATAATGAGAAGAACTCATCTGAAA
57848 GAGTGAGAGT
Statistics
Matches: 152, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
135 3 0.02
136 58 0.38
137 1 0.01
138 1 0.01
139 38 0.25
140 38 0.25
141 13 0.09
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (136 bp):
AATCAACATTTCACATAGAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGGAGAAAAAGTTCA
TAATAAGAAGAACTTGTTCAACCTTCACTCGATTAATCACATATGTTGAATCAGCAACACCTCGC
TTGAGG
Done.