Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004026.1 Hibiscus syriacus cultivar Beakdansim tig00008795_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: 129688
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:192 original size:42 final size:42
Alignment explanation
Indices: 116--204 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
106 GACTCGCCTG
* * *
116 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
158 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
200 TCATC
1 TCATC
205 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1576 original size:13 final size:14
Alignment explanation
Indices: 1543--1576 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1533 ATTGTTTAAT
1543 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
1557 TGA-TTGTAAAA-G
1 TGATTTGTAAAAGG
1569 TGATTTGT
1 TGATTTGT
1577 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 12 0.63
14 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1809 original size:32 final size:32
Alignment explanation
Indices: 1759--1882 Score: 139
Period size: 32 Copynumber: 3.9 Consensus size: 32
1749 ATTAAATTCG
*
1759 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1792 CGTTGCGA-TTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1824 CG-TGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
* *
1856 CGTTGC-AATTTCATTTCACATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1883 AGTAATTTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
30 3 0.04
31 5 0.06
32 56 0.72
33 11 0.14
34 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.41
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1867 original size:64 final size:65
Alignment explanation
Indices: 1752--1881 Score: 208
Period size: 64 Copynumber: 2.0 Consensus size: 65
1742 ACGCGAAATT
* * * *
1752 AAATTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTCATTTCACATTGCG
*
1817 AAATTAGCG-TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCAATTTCATTTCACATTGCG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTCATTTCACATTGCG
1881 A
1 A
1882 TAGTAATTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 52 0.87
65 8 0.13
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTCATTTCACATTGCG
Found at i:4398 original size:23 final size:23
Alignment explanation
Indices: 4367--4411 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4357 ATCATCAAAA
* *
4367 TCCGTGTATTGACCAATATCAAG
1 TCCGGGTATTGACCAAGATCAAG
4390 TCCGGGTATTGACCAAGATCAA
1 TCCGGGTATTGACCAAGATCAA
4412 ATTTCGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (23 bp):
TCCGGGTATTGACCAAGATCAAG
Found at i:5492 original size:20 final size:20
Alignment explanation
Indices: 5457--5494 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5447 ATTCATTTGA
*
5457 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
5477 CTATCGCAATGAGAAAAT
1 CTATCGCAACGAGAAAAT
5495 CGCAATGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:5554 original size:19 final size:19
Alignment explanation
Indices: 5513--5580 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
5503 GAAATGAAAA
5513 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
5529 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5546 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5565 TCGCATTGTGATTTTC
1 TCGCATTGCGATTTTC
5581 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5556 original size:52 final size:52
Alignment explanation
Indices: 5494--5608 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 52
5484 AATGAGAAAA
* ***
5494 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** ** *
5546 TCGCATTGCGATTTTCATTTCGCATTGTGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
5598 TCGCGTTGCGA
1 TCGCATTGCGA
5609 TAGTCTGTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:5716 original size:14 final size:14
Alignment explanation
Indices: 5697--5733 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5687 TATCAATTAA
5697 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5711 ACAAATCATCTTTT
1 ACAAATCAACATTT
5725 ACAAATCAA
1 ACAAATCAA
5734 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:7606 original size:19 final size:20
Alignment explanation
Indices: 7582--7626 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
7572 GAAACTTAAA
7582 ATCGCAACGC-GAAATGACT
1 ATCGCAACGCGGAAATGACT
*
7601 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
7621 ATCGCA
1 ATCGCA
7627 TTGCGATAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:8180 original size:18 final size:18
Alignment explanation
Indices: 8154--8198 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
8144 GTCGATCAGA
*
8154 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
8172 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
8190 TGATGGCTC
1 TGATGGCTC
8199 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:9555 original size:20 final size:20
Alignment explanation
Indices: 9518--9560 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
9508 AATAGTTTCT
*
9518 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCACAACAC
** *
9538 GAAAATGACTATCACAACGC
1 GAAAATGAAAATCACAACAC
9558 GAA
1 GAA
9561 TTCGACTATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCACAACAC
Found at i:10142 original size:20 final size:19
Alignment explanation
Indices: 10036--10150 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
10026 CGCTTTGAAA
*
10036 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
10057 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
10077 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
10097 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
10118 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
10138 ATCGCATTGCGAT
1 ATCGCATTGCGAT
10151 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.07
20 46 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:10168 original size:21 final size:21
Alignment explanation
Indices: 10139--10231 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
10129 ATAGTCAGTA
10139 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
10160 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
10180 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
10201 TCGCGTTGTGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
10221 TCGCATTGCGA
1 TCGCATTGCGA
10232 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:10169 original size:41 final size:41
Alignment explanation
Indices: 10078--10208 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
10068 AAAGTCAGAA
* * * ** *
10078 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
10118 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
10160 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
10201 TCGCGTTG
1 TCGCGTTG
10209 TGATTTACTT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 70 0.93
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:10214 original size:41 final size:41
Alignment explanation
Indices: 10139--10231 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
10129 ATAGTCAGTA
10139 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
10180 TCGCATTGCGATTTTCCCAATTCGCGTTGTGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
10221 TCGCATTGCGA
1 TCGCATTGCGA
10232 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:11294 original size:15 final size:15
Alignment explanation
Indices: 11274--11308 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
11264 GAAGAAGGAA
11274 AACTTGATCTTCCCC
1 AACTTGATCTTCCCC
11289 AACTTGATCTTCCCC
1 AACTTGATCTTCCCC
11304 AACTT
1 AACTT
11309 TATCACTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.37, G:0.06, T:0.34
Consensus pattern (15 bp):
AACTTGATCTTCCCC
Found at i:11650 original size:57 final size:57
Alignment explanation
Indices: 11578--11687 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
11568 GAGCATGATT
* * **
11578 CTATGATATCATCCTTCTTCATGGAGTTGTTGTCTGTAACCTGTGATTAACTCGATG
1 CTATGATATCATCCTTCTTCAGGGAGTTGTTGTCTATAACCTGCAATTAACTCGATG
*
11635 CTATGATATCATCCTTCTTTAGGGAGTTGTTGTCTATAACCTGCAATTAACTC
1 CTATGATATCATCCTTCTTCAGGGAGTTGTTGTCTATAACCTGCAATTAACTC
11688 CCTCCATTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (57 bp):
CTATGATATCATCCTTCTTCAGGGAGTTGTTGTCTATAACCTGCAATTAACTCGATG
Found at i:26332 original size:17 final size:17
Alignment explanation
Indices: 26310--26343 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
26300 CATCGCAAAA
26310 CATAAAA-TAGGACTTTT
1 CATAAAATTA-GACTTTT
26327 CATAAAATTAGACTTTT
1 CATAAAATTAGACTTTT
26344 TTGGTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (17 bp):
CATAAAATTAGACTTTT
Found at i:26431 original size:25 final size:25
Alignment explanation
Indices: 26403--26461 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
26393 ACTCTGTCCG
26403 AGTTGACTCAACGGGTTGACTCACA
1 AGTTGACTCAACGGGTTGACTCACA
*
26428 AGTTGACTCAACGGGTTGACTCACG
1 AGTTGACTCAACGGGTTGACTCACA
26453 AGTTGACTC
1 AGTTGACTC
26462 GATCAACTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (25 bp):
AGTTGACTCAACGGGTTGACTCACA
Found at i:26434 original size:12 final size:13
Alignment explanation
Indices: 26401--26461 Score: 81
Period size: 12 Copynumber: 4.8 Consensus size: 13
26391 TAACTCTGTC
26401 CGAGTTGACTCAA
1 CGAGTTGACTCAA
*
26414 CGGGTTGACTC-A
1 CGAGTTGACTCAA
*
26426 CAAGTTGACTCAA
1 CGAGTTGACTCAA
*
26439 CGGGTTGACTC-A
1 CGAGTTGACTCAA
26451 CGAGTTGACTC
1 CGAGTTGACTC
26462 GATCAACTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
12 21 0.51
13 20 0.49
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (13 bp):
CGAGTTGACTCAA
Found at i:30218 original size:22 final size:22
Alignment explanation
Indices: 30170--30218 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
30160 TGACTTTTTT
*
30170 ATCAATGTCAACGGTCTGACCG
1 ATCAAAGTCAACGGTCTGACCG
* *
30192 GTCAAAGTCAACGGTCTGATCG
1 ATCAAAGTCAACGGTCTGACCG
30214 ATCAA
1 ATCAA
30219 TGGTCAACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (22 bp):
ATCAAAGTCAACGGTCTGACCG
Found at i:33420 original size:2 final size:2
Alignment explanation
Indices: 33413--33437 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33403 ATACGTAAAT
33413 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
33438 TCGTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33510 original size:2 final size:2
Alignment explanation
Indices: 33493--33607 Score: 89
Period size: 2 Copynumber: 58.5 Consensus size: 2
33483 CCTGTTATGC
* **
33493 AT AT AT ACT AT A- AT AT AT AT AT -T AC AT A- AT AT GG AT A- AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
33532 A- AA AT AG AT AT AT AT -T CAC AT ACT AT AT AT AGC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT A-T AT AT AT A-T AT AT AT AT
33573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33608 AACACTTAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
1 6 0.07
2 79 0.88
3 5 0.06
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:34989 original size:13 final size:13
Alignment explanation
Indices: 34967--35002 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
34957 CCTGCATGTA
34967 AATTAATAATAAT
1 AATTAATAATAAT
*
34980 AATTATTAATAAT
1 AATTAATAATAAT
34993 AA-TAATAATA
1 AATTAATAATA
35003 CTAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:34989 original size:16 final size:16
Alignment explanation
Indices: 34968--34998 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34958 CTGCATGTAA
34968 ATTAATAATAATAATT
1 ATTAATAATAATAATT
34984 ATTAATAATAATAAT
1 ATTAATAATAATAAT
34999 AATACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAATAATAATAATT
Found at i:35493 original size:111 final size:111
Alignment explanation
Indices: 35220--35760 Score: 712
Period size: 111 Copynumber: 4.9 Consensus size: 111
35210 TTCAGGAAAG
* * * *
35220 ATTGAATCAGTGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGA-TAGGAAT
1 ATTGAATAAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGG-AT
* *
35284 TTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTAGGAATGTTGATCC
65 TTGTTCCGCTTCTTCTG-AGGGAATATCAGATCTGGGAAAGTTGATCC
*
35332 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATT
1 ATTGAATAAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATT
* * * **
35397 TGTTCCGCTTCCTCTGAGGGAATATCAAATTTGGGAAAGTTGATTT
66 TGTTCCGCTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
* *
35443 ATTAAATAAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATT
1 ATTGAATAAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATT
* ** * *
35508 TGTTTCATTTATTCTGAGGGAATATCAGATCTGAGAAAGTTGATCC
66 TGTTCCGCTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
* * * *
35554 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATC
1 ATTGAATAAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATT
* * *
35619 TGTTCTGCTT-TCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
66 TGTTCCGCTTCT-TCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
* * * *
35665 ATTGAATCAA-GCTAGACTTGTTCCGTTGTTACTCAGGGAATATCAAATCTTGAAAAAG-AGTGA
1 ATTGAAT-AAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAG-GA
* *
35728 TATGTTCCACTTCTTCTGAAGGGAATATCAGAT
64 TTTGTTCCGCTTCTTCTG-AGGGAATATCAGAT
35761 AGATGGATTT
Statistics
Matches: 381, Mismatches: 42, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
110 2 0.01
111 287 0.75
112 89 0.23
113 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (111 bp):
ATTGAATAAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATT
TGTTCCGCTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
Found at i:35636 original size:222 final size:223
Alignment explanation
Indices: 35231--35760 Score: 814
Period size: 222 Copynumber: 2.4 Consensus size: 223
35221 TTGAATCAGT
* * * *
35231 GTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGATAGGAATTTGTTCCGCTTC
1 GTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCACTTC
*
35296 TTCTGAAGGGAATATCAGATCTAGGAATGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGT
66 TTCTGAAGGGAATATCAGATCTAGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGT
* *
35361 CACTCAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTTCCGCTTCCTCTGAGGGAATATCAAA
131 CACTCAGGGAATATCAAATCTTGAAAAAGAAGGATCTGTTCCGCTTCCTCTGAGGGAATATCAAA
* *
35426 TTTGGGAAAGTTGATTTATTAAAT-AAGG
196 TATGGGAAAGTTGATTCATTAAATCAA-G
* * *
35454 GTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTTCATTTA
1 GTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCACTTC
35519 TTCTG-AGGGAATATCAGATCT-GAGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTG
66 TTCTGAAGGGAATATCAGATCTAG-GAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTG
* * * *
35582 TCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTTCTGCTTTCTCTGAGGGAATATCAG
130 TCACTCAGGGAATATCAAATCTTGAAAAAGAAGGATCTGTTCCGCTTCCTCTGAGGGAATATCAA
*
35647 ATATGGGAAAGTTGATTCATTGAATCAAG
195 ATATGGGAAAGTTGATTCATTAAATCAAG
* * * * * *
35676 CTAGACTTGTTCCGTTGTTACTCAGGGAATATCAAATCTTGAAAAAGAGTGATATGTTCCACTTC
1 GTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCACTTC
35741 TTCTGAAGGGAATATCAGAT
66 TTCTGAAGGGAATATCAGAT
35761 AGATGGATTT
Statistics
Matches: 278, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
221 1 0.00
222 198 0.71
223 79 0.28
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (223 bp):
GTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCACTTC
TTCTGAAGGGAATATCAGATCTAGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGT
CACTCAGGGAATATCAAATCTTGAAAAAGAAGGATCTGTTCCGCTTCCTCTGAGGGAATATCAAA
TATGGGAAAGTTGATTCATTAAATCAAG
Found at i:35924 original size:79 final size:79
Alignment explanation
Indices: 35761--35929 Score: 207
Period size: 79 Copynumber: 2.1 Consensus size: 79
35751 AATATCAGAT
** * * *
35761 AGATGGATTTGCTTCACTAGTCTTCCGTGAAGGCTTAAAATGGCCCGGAAGACTTAATCGTCATG
1 AGATGGATTTGCTTCACTACACTTCCGTGAAGGCTTAAAATGGCCCGAAAGACTTAAGCATCATG
* *
35826 CTCGGAATGCTTAT
66 CTCGGAAAGCTTAC
* * * *
35840 TGATGGATTTGCTTCACTACACTTCGGTGAAGGCTTAATATGGCCC-AAAGAATTTAAGCATCAT
1 AGATGGATTTGCTTCACTACACTTCCGTGAAGGCTTAAAATGGCCCGAAAG-ACTTAAGCATCAT
35904 GCTC-GAAAGACTTAC
65 GCTCGGAAAG-CTTAC
35919 AGATGGATTTG
1 AGATGGATTTG
35930 ATCATCATGC
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 7 0.09
79 69 0.91
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (79 bp):
AGATGGATTTGCTTCACTACACTTCCGTGAAGGCTTAAAATGGCCCGAAAGACTTAAGCATCATG
CTCGGAAAGCTTAC
Found at i:35939 original size:34 final size:34
Alignment explanation
Indices: 35898--35984 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
35888 AGAATTTAAG
*
35898 CATCATGCTCGAAAGACTTACAGATGGATTTGAT
1 CATCATGCTCGGAAGACTTACAGATGGATTTGAT
*
35932 CATCATGCTCGGAAGACTTACTGATGGATTTGAT
1 CATCATGCTCGGAAGACTTACAGATGGATTTGAT
35966 CATCATGCTCGGAAGACTT
1 CATCATGCTCGGAAGACTT
35985 CCTAATGACC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (34 bp):
CATCATGCTCGGAAGACTTACAGATGGATTTGAT
Found at i:37306 original size:12 final size:12
Alignment explanation
Indices: 37279--37370 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
37269 ATGGAGATAT
* *
37279 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
37291 CAGAATTCATAT
1 CAGAATTCAGAA
37303 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
37315 CAGAATCCAGAT
1 CAGAATTCAGAA
37327 CAGAA-TCAGAA
1 CAGAATTCAGAA
37338 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
37352 C-GTA-TCAGAA
1 CAGAATTCAGAA
37362 CAGAATTCA
1 CAGAATTCA
37371 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:37311 original size:24 final size:23
Alignment explanation
Indices: 37275--37370 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 23
37265 GTAAATGGAG
*
37275 ATATCAGAAATCAAAACAGAATTC
1 ATATCAG-AATCAGAACAGAATTC
*
37299 ATATCAGATATCAGAACAGAATCC
1 ATATCAGA-ATCAGAACAGAATTC
*
37323 AGATCAGAATCAGAACAGAATTC
1 ATATCAGAATCAGAACAGAATTC
* *
37346 AGGTAAC-GTATCAGAACAGAATTC
1 A--TATCAGAATCAGAACAGAATTC
37370 A
1 A
37371 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
23 16 0.26
24 44 0.71
25 2 0.03
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.20
Consensus pattern (23 bp):
ATATCAGAATCAGAACAGAATTC
Found at i:37358 original size:47 final size:48
Alignment explanation
Indices: 37277--37367 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
37267 AAATGGAGAT
*
37277 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
37325 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
37368 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:37382 original size:24 final size:26
Alignment explanation
Indices: 37273--37384 Score: 98
Period size: 24 Copynumber: 4.7 Consensus size: 26
37263 CGGTAAATGG
*
37273 AGATATCAGAAATCAAAACAGAATTC
1 AGATATCAGAAATCAGAACAGAATTC
* *
37299 --ATATCAGATATCAGAACAGAATCC
1 AGATATCAGAAATCAGAACAGAATTC
37323 AG--ATCAG-AATCAGAACAGAATTC
1 AGATATCAGAAATCAGAACAGAATTC
* * *
37346 AGGTAAC-G-TATCAGAACAGAATTC
1 AGATATCAGAAATCAGAACAGAATTC
*
37370 A-AT-TCGGAAATCAGA
1 AGATATCAGAAATCAGA
37385 TAAAATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.01
23 18 0.26
24 49 0.70
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (26 bp):
AGATATCAGAAATCAGAACAGAATTC
Found at i:38959 original size:19 final size:18
Alignment explanation
Indices: 38937--38975 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
38927 TAAAACAAAC
38937 ATTTCTTATACACATCAAT
1 ATTTCTTAT-CACATCAAT
* *
38956 ATTTTTTATCAGATCAAT
1 ATTTCTTATCACATCAAT
38974 AT
1 AT
38976 GTCTGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTCTTATCACATCAAT
Found at i:39837 original size:13 final size:13
Alignment explanation
Indices: 39819--39879 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
39809 GCCGGTCAAC
39819 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39832 GGTCAATAGGTCGGGTCG
1 GGTC-A-A---CGGGTCG
*
39850 GGTCAACAGGTCG
1 GGTCAACGGGTCG
*
39863 GGTAAACGGGTCG
1 GGTCAACGGGTCG
39876 GGTC
1 GGTC
39880 GGCTATTGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 24 0.62
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.28
ACGTcount: A:0.18, C:0.20, G:0.44, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:39848 original size:18 final size:18
Alignment explanation
Indices: 39825--39865 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
39815 CAACGGTCAA
*
39825 CGGGTCGGGTCAATAGGT
1 CGGGTCGGGTCAACAGGT
39843 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
39861 CGGGT
1 CGGGT
39866 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:39855 original size:31 final size:31
Alignment explanation
Indices: 39819--39881 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
39809 GCCGGTCAAC
* * *
39819 GGTCAACGGGTCGGGTCAATAGGTCGGGTCG
1 GGTCAACAGGTCGGGTAAACAGGTCGGGTCG
*
39850 GGTCAACAGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACAGGTCGGGTAAACAGGTCGGGTCG
39881 G
1 G
39882 CTATTGGTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.46, T:0.17
Consensus pattern (31 bp):
GGTCAACAGGTCGGGTAAACAGGTCGGGTCG
Found at i:42934 original size:300 final size:300
Alignment explanation
Indices: 42392--42987 Score: 1093
Period size: 300 Copynumber: 2.0 Consensus size: 300
42382 CGACTATTCC
*
42392 ATCTGTCAAGATCATAATCATCATTGAACATCATCAATAAAAGTGTGATCTAGTTAGTTTTGTAA
1 ATCTGTCAAGATCATAATCATCATTGAACATCATCAACAAAAGTGTGATCTAGTTAGTTTTGTAA
42457 CATCATACACAAAAAATGCCCCATGTTGTCCGCTCCTATGCACACCTGAATACCAAGCCTATTGT
66 CATCATACACAAAAAATGCCCCATGTTGTCCGCTCCTATGCACACCTGAATACCAAGCCTATTGT
** *
42522 TCATTCCCTTATGATAAAAGAATTTTGTATCGGTCCCTGCAATAAAAATGTATGGTGTTTGATTT
131 TCATTCCCTTATGATAAAAGAAGGTTGTATCGGTCCCTGCAATAAAAATGTATGGTGTTCGATTT
*
42587 TATCTTCTATGGATAAAGTCAAGGTCCCTGTTTTATTAGGTTTCAACCTTGTCATTTTGTCAAAG
196 TATCTTCTATGGATAAAGTCAAGGTCCCTGTTTTATCAGGTTTCAACCTTGTCATTTTGTCAAAG
42652 ATTTATAACTCTAGTCATTTAAAGAATTTTTAATTCGGTT
261 ATTTATAACTCTAGTCATTTAAAGAATTTTTAATTCGGTT
42692 ATCTGTCAAGATCATAATCATCATTGAACATCATCAACAAAAGTGTGATCTAGTTAGTTTTGTAA
1 ATCTGTCAAGATCATAATCATCATTGAACATCATCAACAAAAGTGTGATCTAGTTAGTTTTGTAA
* * *
42757 CATCATACACAAAAGATGCCCCATGTTGTCCGCTCCTATGCATACCTGAATACCGAGCCTATTGT
66 CATCATACACAAAAAATGCCCCATGTTGTCCGCTCCTATGCACACCTGAATACCAAGCCTATTGT
*
42822 TCATTCTCTTATGATAAAAGAAGGTTGTATCGGTCCCTGCAATAAAAATGTATGGTGTTCGATTT
131 TCATTCCCTTATGATAAAAGAAGGTTGTATCGGTCCCTGCAATAAAAATGTATGGTGTTCGATTT
* *
42887 TATCTTCTATGGATAAAGTCAAGGTCCTTGTTTTATCAGGTTTCAACCTTGTCATTTTTTCAAAG
196 TATCTTCTATGGATAAAGTCAAGGTCCCTGTTTTATCAGGTTTCAACCTTGTCATTTTGTCAAAG
42952 ATTTATAACTCTAGTCATTTAAAGAATTTTTAATTC
261 ATTTATAACTCTAGTCATTTAAAGAATTTTTAATTC
42988 AGTTGATATT
Statistics
Matches: 285, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
300 285 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (300 bp):
ATCTGTCAAGATCATAATCATCATTGAACATCATCAACAAAAGTGTGATCTAGTTAGTTTTGTAA
CATCATACACAAAAAATGCCCCATGTTGTCCGCTCCTATGCACACCTGAATACCAAGCCTATTGT
TCATTCCCTTATGATAAAAGAAGGTTGTATCGGTCCCTGCAATAAAAATGTATGGTGTTCGATTT
TATCTTCTATGGATAAAGTCAAGGTCCCTGTTTTATCAGGTTTCAACCTTGTCATTTTGTCAAAG
ATTTATAACTCTAGTCATTTAAAGAATTTTTAATTCGGTT
Found at i:47930 original size:9 final size:9
Alignment explanation
Indices: 47916--47940 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
47906 TTCACATACT
47916 ATATATAGC
1 ATATATAGC
47925 ATATATAGC
1 ATATATAGC
47934 ATATATA
1 ATATATA
47941 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (9 bp):
ATATATAGC
Found at i:49331 original size:13 final size:13
Alignment explanation
Indices: 49313--49340 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49303 CCTGCATGTA
49313 AATTAATAATAAT
1 AATTAATAATAAT
49326 AATTAATAATAAT
1 AATTAATAATAAT
49339 AA
1 AA
49341 AATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:56649 original size:60 final size:60
Alignment explanation
Indices: 56600--56712 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
56590 GTCTTCCGGC
* * **
56600 TATAG-GATATTGGTTTATTGAGTCTCTTGACTATTAAAAATTACAAAATAGTCCCTCAAA
1 TATAGTGA-ATTGCTTTATTGAATCTCTCAACTATTAAAAATTACAAAATAGTCCCTCAAA
*
56660 TATAGTGAATTGCTTTATTGAATCTCTCAACTATTAAAAGTTACAAAATAGTC
1 TATAGTGAATTGCTTTATTGAATCTCTCAACTATTAAAAATTACAAAATAGTC
56713 ACTCGAGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (60 bp):
TATAGTGAATTGCTTTATTGAATCTCTCAACTATTAAAAATTACAAAATAGTCCCTCAAA
Found at i:58534 original size:38 final size:37
Alignment explanation
Indices: 58412--58536 Score: 121
Period size: 39 Copynumber: 3.3 Consensus size: 37
58402 TTTTATATCT
* *
58412 TAATATTTTA-GTTGAACCTAAAATGTTATCAAGAATA
1 TAATATTTTAGGTTAAACC-AAAATGTTATGAAGAATA
*
58449 TAATATTTTCGGTTGGAAACCAGAAAT-TTATGAAGAATA
1 TAATATTTTAGGTT--AAACCA-AAATGTTATGAAGAATA
* * *
58488 TAACATTTTAGGTTCAACCGAAAATGTTAAGAAG-ATA
1 TAATATTTTAGGTTAAACC-AAAATGTTATGAAGAATA
58525 GTAATATTTTAG
1 -TAATATTTTAG
58537 ATTGTGTCCA
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
37 20 0.27
38 21 0.29
39 24 0.33
40 8 0.11
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (37 bp):
TAATATTTTAGGTTAAACCAAAATGTTATGAAGAATA
Found at i:59249 original size:2 final size:2
Alignment explanation
Indices: 59242--59275 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
59232 CTTATGCTTC
59242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59276 TTTTAATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60019 original size:9 final size:8
Alignment explanation
Indices: 60005--60076 Score: 53
Period size: 8 Copynumber: 9.0 Consensus size: 8
59995 TACTATAGTT
60005 TAAAAATGA
1 TAAAAAT-A
60014 TAAAAATA
1 TAAAAATA
60022 T-AAAATA
1 TAAAAATA
60029 -AAATAAGTA
1 TAAA-AA-TA
* *
60038 TAATATTA
1 TAAAAATA
60046 -AAAAATA
1 TAAAAATA
60053 TAAAAATA
1 TAAAAATA
60061 -AAATAATA
1 TAAA-AATA
*
60069 TAACAATA
1 TAAAAATA
60077 AATTGTTTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
7 16 0.31
8 21 0.41
9 12 0.24
10 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:60039 original size:16 final size:16
Alignment explanation
Indices: 60018--60078 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
60008 AAATGATAAA
60018 AATATAA-AATAAAAT
1 AATATAACAATAAAAT
* *
60033 AAGTATAATATTAAAA-
1 AA-TATAACAATAAAAT
*
60049 AATATAAAAATAAAAT
1 AATATAACAATAAAAT
60065 AATATAACAATAAA
1 AATATAACAATAAA
60079 TTGTTTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
15 13 0.33
16 20 0.51
17 6 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AATATAACAATAAAAT
Found at i:60475 original size:2 final size:2
Alignment explanation
Indices: 60468--60493 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60458 ATTTAAAATA
60468 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
60494 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61733 original size:18 final size:19
Alignment explanation
Indices: 61712--61747 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61702 TAATGAAGAT
*
61712 AAAGAC-AATAAGATAAAC
1 AAAGACAAAGAAGATAAAC
61730 AAAGACAAAGAAGATAAA
1 AAAGACAAAGAAGATAAA
61748 GATAGGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.69, C:0.08, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAGACAAAGAAGATAAAC
Found at i:62772 original size:16 final size:17
Alignment explanation
Indices: 62751--62784 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
62741 CTTTTTTTAA
62751 AAAAATAA-AACAAAAG
1 AAAAATAAGAACAAAAG
*
62767 AAAAATAAGATCAAAAG
1 AAAAATAAGAACAAAAG
62784 A
1 A
62785 GGTGAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAAATAAGAACAAAAG
Found at i:64902 original size:113 final size:112
Alignment explanation
Indices: 64704--64921 Score: 321
Period size: 113 Copynumber: 1.9 Consensus size: 112
64694 TAGTATGTAA
64704 CTTGATATCGCTTAATCAAAGTCTCGATTTCGAGTCATTGTACATGCAAAAAATCCATGTAGGGA
1 CTTGATATCGCTTAATCAAAGTCTCGATTTCGAGTCATTGTACATGCAAAAAATCCA-GTAGGGA
* *
64769 GACTCACTCAGTAAAATCAGGTGTGCGACACATGTCAATTTGGATTAG
65 GACTCACTCACTAAAATCAGGTGTGCGACACATGCCAATTTGGATTAG
* * ** *
64817 CTTGATATCGCTTAATTAAGGTCTCGATTTCGAGTCATTGTGTATGCAAAAAATATCC-GTTGGG
1 CTTGATATCGCTTAATCAAAGTCTCGATTTCGAGTCATTGTACATGC-AAAAA-ATCCAGTAGGG
* *
64881 AGACTTACTTACTAAAATCAGGTGTGCGACACATGCCAATT
64 AGACTCACTCACTAAAATCAGGTGTGCGACACATGCCAATT
64922 CAGATTAATC
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
113 85 0.90
114 5 0.05
115 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (112 bp):
CTTGATATCGCTTAATCAAAGTCTCGATTTCGAGTCATTGTACATGCAAAAAATCCAGTAGGGAG
ACTCACTCACTAAAATCAGGTGTGCGACACATGCCAATTTGGATTAG
Found at i:78527 original size:27 final size:27
Alignment explanation
Indices: 78497--78550 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
78487 CTTATTTTAA
78497 AAAAAACC-CAAAATATTT-AGAAATCTT
1 AAAAAACCTCAAAAT-TTTGA-AAATCTT
*
78524 AAAAGACCTCAAAATTTTGAAAATCTT
1 AAAAAACCTCAAAATTTTGAAAATCTT
78551 GATTCCAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.28
Consensus pattern (27 bp):
AAAAAACCTCAAAATTTTGAAAATCTT
Found at i:83847 original size:21 final size:21
Alignment explanation
Indices: 83821--83860 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
83811 TACCGTCCGT
83821 GGACTTATAATATCTTCGCAC
1 GGACTTATAATATCTTCGCAC
83842 GGACTTATAATATCTTCGC
1 GGACTTATAATATCTTCGC
83861 GTATTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (21 bp):
GGACTTATAATATCTTCGCAC
Found at i:86114 original size:34 final size:34
Alignment explanation
Indices: 86066--86141 Score: 127
Period size: 34 Copynumber: 2.2 Consensus size: 34
86056 TAGGGTTTCA
86066 GGTCAGATCTGGGCTTCT-GGTTGTAGCTAGGTTG
1 GGTCAGATCTGGGCTT-TGGGTTGTAGCTAGGTTG
*
86100 GGTCGGATCTGGGCTTTGGGTTGTAGCTAGGTTG
1 GGTCAGATCTGGGCTTTGGGTTGTAGCTAGGTTG
86134 GGTCAGAT
1 GGTCAGAT
86142 ATGGCTCCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 1 0.03
34 38 0.97
ACGTcount: A:0.12, C:0.13, G:0.41, T:0.34
Consensus pattern (34 bp):
GGTCAGATCTGGGCTTTGGGTTGTAGCTAGGTTG
Found at i:86136 original size:16 final size:16
Alignment explanation
Indices: 86084--86136 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
86074 CTGGGCTTCT
86084 GGTTGTAGCTAGGTTG
1 GGTTGTAGCTAGGTTG
* * * *
86100 GGTCGGATCTGGGCTTTG
1 GGTTGTAGCTAGG--TTG
86118 GGTTGTAGCTAGGTTG
1 GGTTGTAGCTAGGTTG
86134 GGT
1 GGT
86137 CAGATATGGC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
16 15 0.56
18 12 0.44
ACGTcount: A:0.09, C:0.09, G:0.45, T:0.36
Consensus pattern (16 bp):
GGTTGTAGCTAGGTTG
Found at i:88327 original size:3 final size:3
Alignment explanation
Indices: 88319--88411 Score: 104
Period size: 3 Copynumber: 31.3 Consensus size: 3
88309 CTACCAAAAA
* *
88319 TAT TAT TA- TAT TAA TAT TAT TATT TAT TAT TA- TAT TAA TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
88362 ATAT TAA TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
88408 TAT T
1 TAT T
88412 TTGTTACATA
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
2 7 0.09
3 63 0.82
4 7 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:88392 original size:50 final size:51
Alignment explanation
Indices: 88317--88412 Score: 144
Period size: 50 Copynumber: 1.9 Consensus size: 51
88307 GTCTACCAAA
88317 AATATTATTATATTAATATTATTATTTATTATTA-TATTAA-TATTTATATT
1 AATATTATTATATTAATATTATTA-TTATTATTATTATTAATTATTTATATT
*
88367 AATATTATTATTATT-TTATTATTATTATTATTATTATTAATTATTT
1 AATATTATTA-TATTAATATTATTATTATTATTATTATTAATTATTT
88413 TGTTACATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
49 9 0.21
50 24 0.57
51 9 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (51 bp):
AATATTATTATATTAATATTATTATTATTATTATTATTAATTATTTATATT
Found at i:92433 original size:17 final size:17
Alignment explanation
Indices: 92411--92447 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
92401 CAACAAAGAG
*
92411 AAAAAGATCAAAGAAAA
1 AAAAAGAACAAAGAAAA
92428 AAAAAGAACAAAGAAAA
1 AAAAAGAACAAAGAAAA
92445 AAA
1 AAA
92448 TTAAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.81, C:0.05, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAGAACAAAGAAAA
Found at i:93648 original size:65 final size:65
Alignment explanation
Indices: 93550--93750 Score: 184
Period size: 64 Copynumber: 3.1 Consensus size: 65
93540 GTTTTCTTAA
* *
93550 AAACAAA-TTTTGTCTCTC--GAGACAGTTTATTTTGAAAAAATATCTTTGAGTCTGTTTCTTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAATATCTTTGAGTCTGTTTCTTTG
* * *
93612 GAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAA-A-CTTTGAGTTTCTTTCCTT
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGA-AAAAATATCTTTGAGTCTGTTT-CTT
93675 TG
64 TG
* * * * *
93677 AAAC-AAGTTTAGTCTC-CATTGAGACATTTTTCTCTT-AAAACACTTATATTTGAGTCTGTTTC
1 AAACAAAGTTTTGTCTCTC-TTGAGACA-ATTTCTTTTGAAAA-A-ATATCTTTGAGTCTGTTT-
*
93739 CCTTG
61 CTTTG
93744 AAACAAA
1 AAACAAA
93751 ACAAACATCT
Statistics
Matches: 113, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
62 6 0.05
63 15 0.13
64 33 0.29
65 31 0.27
66 6 0.05
67 20 0.18
68 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (65 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAATATCTTTGAGTCTGTTTCTTTG
Found at i:93801 original size:102 final size:101
Alignment explanation
Indices: 93668--93852 Score: 234
Period size: 102 Copynumber: 1.8 Consensus size: 101
93658 TTTGAGTTTC
* *
93668 TTTCCTTTGAAACAAGTTTAGTCTCCATTGAGACATTTTTCTCTT-AAAACACTTATATTTGAGT
1 TTTCCCTTGAAACAAGTTTAGTCTCCATTGAGACA-TTTTCTCTTGAAAA-A-TCATATTTGAGT
*
93732 CTGTTTCCCTTGAAA-CAAAACAAACATCTTTGATATCG
63 CGGTTTCCCTTGAAACCAAAACAAACATCTTTGATATCG
* * *
93770 TTTCCCTTGAAACGAA-TTTTGTCTCTC-TTGAGACATTTTCTTTTGAAAAATCATCTTTGAGTC
1 TTTCCCTTGAAAC-AAGTTTAGTCTC-CATTGAGACATTTTCTCTTGAAAAATCATATTTGAGTC
*
93833 GGTTTCTCTTGAAACCAAAA
64 GGTTTCCCTTGAAACCAAAA
93853 TCCTTAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
100 23 0.32
101 14 0.19
102 32 0.44
103 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (101 bp):
TTTCCCTTGAAACAAGTTTAGTCTCCATTGAGACATTTTCTCTTGAAAAATCATATTTGAGTCGG
TTTCCCTTGAAACCAAAACAAACATCTTTGATATCG
Found at i:94091 original size:131 final size:131
Alignment explanation
Indices: 93852--94118 Score: 332
Period size: 131 Copynumber: 2.0 Consensus size: 131
93842 TGAAACCAAA
* * ** * *
93852 ATCCTTAAAGATGGCATGCCGTCCTCATCGTGTAGGAACCGTGTCATCCCCCAACCATGTCTCCT
1 ATCCCTAAAGATGGCATACCGTCCTCATCACGTAGGAACCATGTCATCCCCCAACCATGCCTCCT
* * *
93917 CATCACGTAGGAGTCGCATCAACCTTAGATAACCAGCTGTCCTCAT-TACGTAGGAATCATGTTA
66 CATCACGTAGGAGTCGCATCAACCCTAGATAACCAGCTGTCCTCATCGA-GTAGGAACCATGTTA
93981 TC
130 TC
*
93983 ATCCCTAAAGATGGCATACCGTCCTCATCACGTAGGAACCATGTCATCCCCCCGACCA-GACCTC
1 ATCCCTAAAGATGGCATACCGTCCTCATCACGTAGGAACCATGTCAT-CCCCCAACCATG-CCTC
*
94047 CTCATCACGTAGGAG-C-CATGTC-ACCCTAGATAACCAG-TCGTCCTCATCGAGTAGGAACCGT
64 CTCATCACGTAGGAGTCGCA--TCAACCCTAGATAACCAGCT-GTCCTCATCGAGTAGGAACCAT
94108 GTTATC
126 GTTATC
94114 A-CCCT
1 ATCCCT
94119 TCCTAAAGAT
Statistics
Matches: 119, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
130 7 0.06
131 82 0.69
132 30 0.25
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCATACCGTCCTCATCACGTAGGAACCATGTCATCCCCCAACCATGCCTCCT
CATCACGTAGGAGTCGCATCAACCCTAGATAACCAGCTGTCCTCATCGAGTAGGAACCATGTTAT
C
Found at i:95934 original size:30 final size:30
Alignment explanation
Indices: 95892--96049 Score: 140
Period size: 30 Copynumber: 5.2 Consensus size: 30
95882 TGTTTATTAG
*
95892 GTCCTTCT-AGTTTCTGTTTTTACTATTTTA
1 GTCCTT-TAAGTTTCTGTTTTTTCTATTTTA
* * * *
95922 GCCCTTTAAGTTTTTATTTTTTCCATTTTA
1 GTCCTTTAAGTTTCTGTTTTTTCTATTTTA
* * * *
95952 TTCCTTTAAATTTTTGTTGTTTATGCCATTTTA
1 GTCCTTTAAGTTTCTGTT-TTT-T-CTATTTTA
95985 GTCCTTTAAGTTT-TGGTTTTTTCTATTTTA
1 GTCCTTTAAGTTTCT-GTTTTTTCTATTTTA
* ** *
96015 GTCTTTTAAGTTTCCATTTTTTCTATTTTG
1 GTCCTTTAAGTTTCTGTTTTTTCTATTTTA
96045 GTCCT
1 GTCCT
96050 CATGTGTTTG
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
29 1 0.01
30 73 0.70
31 4 0.04
32 5 0.05
33 22 0.21
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (30 bp):
GTCCTTTAAGTTTCTGTTTTTTCTATTTTA
Found at i:97020 original size:26 final size:22
Alignment explanation
Indices: 96990--97046 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 22
96980 AATCACTAAT
96990 TTTTTAAAATAAAAATGTCATAATTA
1 TTTTTAAAAT-AAAAT-T--TAATTA
*
97016 TTTTTAAAATAATATTTAATTA
1 TTTTTAAAATAAAATTTAATTA
97038 TTTTTAAAA
1 TTTTTAAAA
97047 ATGGTTATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 15 0.50
24 1 0.03
25 4 0.13
26 10 0.33
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTAAAATAAAATTTAATTA
Found at i:102606 original size:15 final size:15
Alignment explanation
Indices: 102588--102622 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
102578 AATCTATCAA
* *
102588 GTCTACTGTTATCTG
1 GTCTACTATTATATG
102603 GTCTACTATTATATG
1 GTCTACTATTATATG
102618 GTCTA
1 GTCTA
102623 TTCTTCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (15 bp):
GTCTACTATTATATG
Found at i:103442 original size:19 final size:19
Alignment explanation
Indices: 103396--103449 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
103386 TTAGCCCAAG
*
103396 AGTATCGATACTCCTACAAA
1 AGTATCGATACT-TTACAAA
* * *
103416 AGTTTCGATACTTTATATA
1 AGTATCGATACTTTACAAA
103435 AGTATCGATACTTTA
1 AGTATCGATACTTTA
103450 AACATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (19 bp):
AGTATCGATACTTTACAAA
Found at i:104679 original size:18 final size:19
Alignment explanation
Indices: 104627--104680 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
104617 ATTTTCAATG
104627 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
104646 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATACCAATTGTTA
*
104666 AAAAATATACCAATT
1 AAAAAGATACCAATT
104681 ATTGGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 8 0.27
19 5 0.17
20 5 0.17
21 12 0.40
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.28
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:104845 original size:18 final size:19
Alignment explanation
Indices: 104801--104896 Score: 124
Period size: 21 Copynumber: 4.9 Consensus size: 19
104791 ATGTTTAATG
104801 AAAAAGATATCAATTGTTAA
1 AAAAAGATATCAATTGTT-A
104821 CAAAAAGATATCAATTGTT-
1 -AAAAAGATATCAATTGTTA
*
104840 AAAAAGATACCAATTGTTAA
1 AAAAAGATATCAATTGTT-A
104860 CAAAAAGATATCAATTGTT-
1 -AAAAAGATATCAATTGTTA
*
104879 AAAAAGATACCAATTGTT
1 AAAAAGATATCAATTGTT
104897 GGAAAATATA
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
18 34 0.49
21 35 0.51
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:104855 original size:39 final size:39
Alignment explanation
Indices: 104801--104896 Score: 183
Period size: 39 Copynumber: 2.5 Consensus size: 39
104791 ATGTTTAATG
*
104801 AAAAAGATATCAATTGTTAACAAAAAGATATCAATTGTT
1 AAAAAGATACCAATTGTTAACAAAAAGATATCAATTGTT
104840 AAAAAGATACCAATTGTTAACAAAAAGATATCAATTGTT
1 AAAAAGATACCAATTGTTAACAAAAAGATATCAATTGTT
104879 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
104897 GGAAAATATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.29
Consensus pattern (39 bp):
AAAAAGATACCAATTGTTAACAAAAAGATATCAATTGTT
Found at i:108094 original size:21 final size:20
Alignment explanation
Indices: 107987--108126 Score: 174
Period size: 20 Copynumber: 6.8 Consensus size: 20
107977 TCGAAATGGA
* *
107987 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTGCAGG
*
108007 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCAC---T-GCAGG
108030 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
108050 GTGCATGGATGCATTGCAGG
1 GTGCATGGATGCACTGCAGG
108070 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCA-GG
*
108091 GTGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTGCA-GG
108112 GTGCATGGATGCACT
1 GTGCATGGATGCACT
108127 TTGACACCCT
Statistics
Matches: 108, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.03
20 51 0.47
21 37 0.34
23 15 0.14
24 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:118953 original size:60 final size:60
Alignment explanation
Indices: 118883--119003 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
118873 GTCTATCTAA
* * * * *
118883 GACAGTACTTCTCTCATTTC-AGCATTTTGACCTCTAAAGATTATTATTTTTCTAAATAGC
1 GACAGCACTTCTCACATTTCGA-CATTTTGACCCCTAAACATTATTATTTTTCTAAAAAGC
118943 GACAGCACTTCTCACATTTCGACATTTTGACCCCTAAACATTATTATTTTTCTAAAAAGC
1 GACAGCACTTCTCACATTTCGACATTTTGACCCCTAAACATTATTATTTTTCTAAAAAGC
119003 G
1 G
119004 TACCTGAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (60 bp):
GACAGCACTTCTCACATTTCGACATTTTGACCCCTAAACATTATTATTTTTCTAAAAAGC
Found at i:121894 original size:3 final size:3
Alignment explanation
Indices: 121886--121910 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
121876 TACATAATGT
121886 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
121911 GTAACGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:122811 original size:40 final size:39
Alignment explanation
Indices: 122767--122908 Score: 98
Period size: 40 Copynumber: 3.6 Consensus size: 39
122757 CATATTAACA
122767 ATATAAGAATAAATAATATATATATAGATAAATAAAAGTT
1 ATATAA-AATAAATAATATATATATAGATAAATAAAAGTT
* * * *
122807 ATATATACAA-AAATAATAAATAATATA-AT-AATGAATGATA
1 ATATA-A-AATAAATAATATAT-ATATAGATAAATAAAAG-TT
* * **
122847 AAATAAAATATAT-ATATATA-AT-GAATACGTAAAAGTT
1 ATATAAAATAAATAATATATATATAG-ATAAATAAAAGTT
* *
122884 ATATAATATAATTAATATATATATA
1 ATATAAAATAAATAATATATATATA
122909 TATATATATA
Statistics
Matches: 75, Mismatches: 17, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
36 2 0.03
37 13 0.17
38 18 0.24
39 12 0.16
40 22 0.29
41 8 0.11
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (39 bp):
ATATAAAATAAATAATATATATATAGATAAATAAAAGTT
Found at i:122903 original size:2 final size:2
Alignment explanation
Indices: 122883--122947 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
122873 ACGTAAAAGT
122883 TA TA TA -A TA TA -A T- TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122921 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
122948 GAAAAACTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 4 0.07
2 55 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:129407 original size:21 final size:21
Alignment explanation
Indices: 129381--129455 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
129371 TCAAGTCTTC
*
129381 AGTATGGATATCAGTTCATCT
1 AGTATGGATACCAGTTCATCT
**
129402 AGTATGGATACCAACTCATCT
1 AGTATGGATACCAGTTCATCT
* * * *
129423 GGTATGGACACCAGTTTATCC
1 AGTATGGATACCAGTTCATCT
*
129444 AGTATAGATACC
1 AGTATGGATACC
129456 CACTGTTATA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (21 bp):
AGTATGGATACCAGTTCATCT
Done.