Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002399.1 Hibiscus syriacus cultivar Beakdansim tig00004909_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: 158962
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4590 original size:19 final size:19
Alignment explanation
Indices: 4563--4620 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
4553 CGAAAAACCG
4563 ACCCGAACCGAACCGAAAA
1 ACCCGAACCGAACCGAAAA
* *
4582 ACTCGAACCGTTA---AAAA
1 ACCCGAACCG-AACCGAAAA
4599 ACCCGAACCGAACCGAAAA
1 ACCCGAACCGAACCGAAAA
4618 ACC
1 ACC
4621 GGTTTCGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.03
17 13 0.42
19 16 0.52
20 1 0.03
ACGTcount: A:0.47, C:0.34, G:0.14, T:0.05
Consensus pattern (19 bp):
ACCCGAACCGAACCGAAAA
Found at i:7793 original size:2 final size:2
Alignment explanation
Indices: 7786--7821 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7776 GGGCAGCCAA
7786 AT 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 AT
7822 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12977 original size:57 final size:53
Alignment explanation
Indices: 12883--13149 Score: 334
Period size: 57 Copynumber: 5.0 Consensus size: 53
12873 TCGATTTGCG
* *
12883 AAATTCGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAA
1 AAATTCG-GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
*
12937 ACGGAATTCGTGTTGCGATAGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCG--A
1 A---AATTCG-GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
* *
12992 AAA--CGGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAA
1 AAATTCGGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
* *
13043 ACGGAATTCGTGTTGCGTTAGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCG--A
1 A---AATTCG-GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
13098 AAA--CGGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
1 AAATTCGGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
13149 A
1 A
13150 TTTCCATGTT
Statistics
Matches: 187, Mismatches: 13, Indels: 29
0.82 0.06 0.13
Matches are distributed among these distances:
49 81 0.43
50 4 0.02
51 4 0.02
52 4 0.02
54 3 0.02
55 4 0.02
56 2 0.01
57 85 0.45
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (53 bp):
AAATTCGGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAA
Found at i:13020 original size:49 final size:49
Alignment explanation
Indices: 12948--13149 Score: 287
Period size: 49 Copynumber: 4.0 Consensus size: 49
12938 CGGAATTCGT
*
12948 GTTGCGATAGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACG
1 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACG
* *
12997 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAAACGGAATTCG
1 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCG--AA---AA--CG
* *
13053 TGTTGCGTTAGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACG
1 -GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACG
13103 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAA
1 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAA
13150 TTTCCATGTT
Statistics
Matches: 136, Mismatches: 9, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
49 85 0.62
50 2 0.01
51 2 0.01
52 2 0.01
54 2 0.01
55 2 0.01
56 2 0.01
57 39 0.29
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (49 bp):
GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACG
Found at i:13076 original size:106 final size:106
Alignment explanation
Indices: 12891--13149 Score: 491
Period size: 106 Copynumber: 2.4 Consensus size: 106
12881 CGAAATTCGC
12891 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAAACGGAATTCGTGTTGCGAT
1 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAAACGGAATTCGTGTTGCGAT
12956 AGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACG
66 AGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACG
*
12997 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAAACGGAATTCGTGTTGCGTT
1 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAAACGGAATTCGTGTTGCGAT
13062 AGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACG
66 AGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACG
* *
13103 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAA
1 GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAAA
13150 TTTCCATGTT
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 150 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (106 bp):
GTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCATTACGAAAACGGAATTCGTGTTGCGAT
AGTTGTGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACG
Found at i:16618 original size:24 final size:24
Alignment explanation
Indices: 16591--16641 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
16581 CTTTGATTTG
16591 TCTATACTCTCATTGATAATTTTT
1 TCTATACTCTCATTGATAATTTTT
16615 TCTATACTCTCATTGATAATTTTT
1 TCTATACTCTCATTGATAATTTTT
16639 TCT
1 TCT
16642 CAAATTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.55
Consensus pattern (24 bp):
TCTATACTCTCATTGATAATTTTT
Found at i:22679 original size:15 final size:16
Alignment explanation
Indices: 22659--22702 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
22649 CGGGTATCCG
22659 CGATTTTTGGGTA-TT
1 CGATTTTTGGGTATTT
*
22674 CGATTTTTAGGTATTT
1 CGATTTTTGGGTATTT
*
22690 TGAATTTTTGGGT
1 CG-ATTTTTGGGT
22703 CGATGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 3 0.12
17 9 0.38
ACGTcount: A:0.16, C:0.05, G:0.25, T:0.55
Consensus pattern (16 bp):
CGATTTTTGGGTATTT
Found at i:23730 original size:2 final size:2
Alignment explanation
Indices: 23723--23747 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23713 AAGCATTATC
23723 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
23748 TTTGGGTAAA
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:37134 original size:60 final size:58
Alignment explanation
Indices: 36968--37152 Score: 173
Period size: 60 Copynumber: 3.1 Consensus size: 58
36958 GCATATGCCA
* * * * *
36968 ATAGTTTGAGATGAAATTGAAATGCTCAAAAGTTTAGGAAAT-AATTTAGAATGATAATC
1 ATAGTTTGAGATAAAATTGAAAT-TTCAAAAGTTTA-GAGATCAATTTAGAATAAGAATC
* *
37027 ATAATTTGAGTATAAAATT-AGAATTCTCAAAAGTTT-GAAGA-CTAATTTAGAATAAGAATT
1 ATAGTTTGAG-ATAAAATTGA-AATT-TCAAAAGTTTAG-AGATC-AATTTAGAATAAGAATC
*
37087 ATAGTTTGAGAATAAAATTGAAATATTCAAAAGTTTAGAGATCAATTTA-AAGTAAGAACC
1 ATAGTTTGAG-ATAAAATTGAAAT-TTCAAAAGTTTAGAGATCAATTTAGAA-TAAGAATC
37147 ATAGTT
1 ATAGTT
37153 GGAGGGCATA
Statistics
Matches: 104, Mismatches: 11, Indels: 21
0.76 0.08 0.15
Matches are distributed among these distances:
58 1 0.01
59 14 0.13
60 85 0.82
61 4 0.04
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (58 bp):
ATAGTTTGAGATAAAATTGAAATTTCAAAAGTTTAGAGATCAATTTAGAATAAGAATC
Found at i:38549 original size:61 final size:62
Alignment explanation
Indices: 38441--38566 Score: 193
Period size: 61 Copynumber: 2.0 Consensus size: 62
38431 TATTCTTTTA
* *
38441 ATAATTCAATTTAAAAAAGTATTTGTTATTTTTTTTAATTTTAAATATTAAAAAATAATTAT
1 ATAAGTCAATTTAAAAAAGTATTTGTTATTCTTTTTAATTTTAAATATTAAAAAATAATTAT
* *
38503 ATAAGTCAATTT-AAAAAGATATTTGTTA-TCTTTTTAATTTTGAATATTAAAAGATAATTAT
1 ATAAGTCAATTTAAAAAAG-TATTTGTTATTCTTTTTAATTTTAAATATTAAAAAATAATTAT
38564 ATA
1 ATA
38567 TTTTATATGT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 39 0.66
62 20 0.34
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (62 bp):
ATAAGTCAATTTAAAAAAGTATTTGTTATTCTTTTTAATTTTAAATATTAAAAAATAATTAT
Found at i:38600 original size:22 final size:21
Alignment explanation
Indices: 38574--38614 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38564 ATATTTTATA
38574 TGTTTCAAATTAAAATAATATT
1 TGTTT-AAATTAAAATAATATT
* *
38596 TGTTTAAGTTTAAATAATA
1 TGTTTAAATTAAAATAATA
38615 AAAGGAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (21 bp):
TGTTTAAATTAAAATAATATT
Found at i:41199 original size:10 final size:10
Alignment explanation
Indices: 41149--41182 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
41139 ACACGCTTGG
41149 CATCCGAGGC
1 CATCCGAGGC
41159 CATCCGAGAG-
1 CATCCGAG-GC
41169 CATCCGAGGC
1 CATCCGAGGC
41179 CATC
1 CATC
41183 TGACCGAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:41238 original size:33 final size:33
Alignment explanation
Indices: 41186--41270 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
41176 GGCCATCTGA
* * * *
41186 CCGAGGCCATCCGAACGAGCTATGTGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGTGAGGGAAT
41219 CCGAGGGCAACCGAGCGAGCTATGTGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGTGAGGGAAT
*
41252 CCGAGAG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
41271 GGTAGGTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.27, C:0.25, G:0.38, T:0.11
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGTGAGGGAAT
Found at i:41307 original size:29 final size:29
Alignment explanation
Indices: 41274--41329 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
41264 GAGCGAGGGT
*
41274 AGGTCACCCGGAGTGCATAG-CGACCTACA
1 AGGTCACCCGGAGGGCAT-GTCGACCTACA
**
41303 AGGTCGTCCGGAGGGCATGTCGACCTA
1 AGGTCACCCGGAGGGCATGTCGACCTA
41330 TGTGTTGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (29 bp):
AGGTCACCCGGAGGGCATGTCGACCTACA
Found at i:41430 original size:29 final size:29
Alignment explanation
Indices: 41388--41444 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
41378 GAGCAAGGGT
41388 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
41417 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
41445 GGCCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:42861 original size:12 final size:12
Alignment explanation
Indices: 42844--42868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42834 TTCAAATCTA
42844 AAGAAAATTAAG
1 AAGAAAATTAAG
42856 AAGAAAATTAAG
1 AAGAAAATTAAG
42868 A
1 A
42869 GACTTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAGAAAATTAAG
Found at i:43167 original size:18 final size:19
Alignment explanation
Indices: 43125--43169 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
43115 TTTGGTTCAC
*
43125 GGAATATAAGATTAGCAGTG
1 GGAATATAAGATTACCAG-G
*
43145 GGAATGTAAGATTACCA-G
1 GGAATATAAGATTACCAGG
43163 GGAATAT
1 GGAATAT
43170 GATTACTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:44435 original size:21 final size:20
Alignment explanation
Indices: 44411--44520 Score: 66
Period size: 21 Copynumber: 5.3 Consensus size: 20
44401 ATTGGAATGA
44411 ATCGCAACGCGAACTTCGCCT
1 ATCGCAA-GCGAACTTCGCCT
* * **
44432 ATCGCAA-CG-ATTTGGAAT
1 ATCGCAAGCGAACTTCGCCT
44450 GAATCGCAAAGCGAACTTCGCCT
1 --ATCGC-AAGCGAACTTCGCCT
* **
44473 ATCGCAA-CGAA-TTGGAAT
1 ATCGCAAGCGAACTTCGCCT
44491 GAATCGCAATGCGAACTTCGCCT
1 --ATCGCAA-GCGAACTTCGCCT
44514 ATCGCAA
1 ATCGCAA
44521 CGATTTGGAA
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
18 9 0.14
19 6 0.09
20 14 0.22
21 21 0.32
22 6 0.09
23 9 0.14
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAAGCGAACTTCGCCT
Found at i:44453 original size:41 final size:41
Alignment explanation
Indices: 44396--44601 Score: 340
Period size: 41 Copynumber: 5.0 Consensus size: 41
44386 CATGGGCCAA
*
44396 AACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
1 AACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
*
44437 AACGATTTGGAATGAATCGCAAAGCGAACTTCGCCTATCGC
1 AACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
* *
44478 AACGAATTGGAATGAATCGCAATGCGAACTTCGCCTATCGC
1 AACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
*
44519 AACGATTTGGAATGAATCGCAACGCGAACTTCGACTATCGC
1 AACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
* *
44560 AACGAATTTGGAATGAATCGCAATGCGAACTTCGACTATCGC
1 AACG-ATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
44602 GTTGCGAATA
Statistics
Matches: 156, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
41 120 0.77
42 36 0.23
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (41 bp):
AACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
Found at i:44646 original size:15 final size:16
Alignment explanation
Indices: 44621--44650 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44611 AGAGGTGTGC
44621 AAATCTGGGTACCCGA
1 AAATCTGGGTACCCGA
44637 AAAT-TGGGTACCCG
1 AAATCTGGGTACCCG
44651 GAACTTCCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (16 bp):
AAATCTGGGTACCCGA
Found at i:45395 original size:63 final size:62
Alignment explanation
Indices: 45292--45434 Score: 164
Period size: 63 Copynumber: 2.3 Consensus size: 62
45282 AAAAAATTAA
**
45292 TTTTTATTGTAATATAATTAACTTTTAAACAGTTTGGGTGGACGA-AAATAAAAAAACTAATGT
1 TTTTTATTGTAATATAATTAACTTTTAAACAGTTCAGGTGGACGACAAAT-AAAAAACTAAT-T
* * * * *
45355 TTTTTATTCG-AATATAATTAATTTTTAAATAGTTCAGGTGGGCTACAAATCAAAAACTAATT
1 TTTTTATT-GTAATATAATTAACTTTTAAACAGTTCAGGTGGACGACAAATAAAAAACTAATT
*
45417 TTTTTCATTATAATATAA
1 TTTTT-ATTGTAATATAA
45435 CAATGTTATC
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
62 6 0.09
63 57 0.84
64 5 0.07
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (62 bp):
TTTTTATTGTAATATAATTAACTTTTAAACAGTTCAGGTGGACGACAAATAAAAAACTAATT
Found at i:46429 original size:9 final size:8
Alignment explanation
Indices: 46400--46445 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
46390 AGTAGTAAGA
46400 AGATGAAT
1 AGATGAAT
*
46408 -GATGAAA
1 AGATGAAT
46415 AGATGAACT
1 AGATGAA-T
46424 AGATGAAT
1 AGATGAAT
*
46432 -GATGAAA
1 AGATGAAT
46439 AGATGAA
1 AGATGAA
46446 CTCTCAACGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
7 12 0.38
8 13 0.41
9 7 0.22
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.20
Consensus pattern (8 bp):
AGATGAAT
Found at i:46432 original size:24 final size:24
Alignment explanation
Indices: 46400--46447 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
46390 AGTAGTAAGA
46400 AGATGAATGATGAAAAGATGAACT
1 AGATGAATGATGAAAAGATGAACT
46424 AGATGAATGATGAAAAGATGAACT
1 AGATGAATGATGAAAAGATGAACT
46448 CTCAACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.25, T:0.21
Consensus pattern (24 bp):
AGATGAATGATGAAAAGATGAACT
Found at i:48989 original size:57 final size:57
Alignment explanation
Indices: 48921--49121 Score: 208
Period size: 57 Copynumber: 3.5 Consensus size: 57
48911 ATGTTCTAAA
** * *
48921 ATCGCAACGCGAATAGGTAAA-TCGCAACGCTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAACGCGAAT-TCTAAATTCGTAACGCTAATTACCGATATAGGTAAACACTACT
* *
48978 ATCGCAACGCG-ATTTTCAAATTCGTAACGCTAATTACCGATATAGGTAAACATTACT
1 ATCGCAACGCGAATTCT-AAATTCGTAACGCTAATTACCGATATAGGTAAACACTACT
* * * * * * *
49035 ATCACAAAGCGATTTTCAAAATTCGTAACGCTAATTACCGACATAGGGAAATACTACT
1 ATCGCAACGCGA-ATTCTAAATTCGTAACGCTAATTACCGATATAGGTAAACACTACT
* * * *
49093 ATCGCAACACGATTTTTAAATTCGCAACG
1 ATCGCAACGCGAATTCTAAATTCGTAACG
49122 TTATTTTCAC
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
55 1 0.01
56 5 0.04
57 68 0.56
58 45 0.37
59 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (57 bp):
ATCGCAACGCGAATTCTAAATTCGTAACGCTAATTACCGATATAGGTAAACACTACT
Found at i:49093 original size:58 final size:57
Alignment explanation
Indices: 48946--49121 Score: 246
Period size: 57 Copynumber: 3.1 Consensus size: 57
48936 GGTAAATCGC
* *
48946 AACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTTCAAATTCGT
1 AACGCTAATTACCGATATAGGTAAACACTACTATCGCAAAGCGATTTTCAAATTCGT
* *
49003 AACGCTAATTACCGATATAGGTAAACATTACTATCACAAAGCGATTTTCAAAATTCGT
1 AACGCTAATTACCGATATAGGTAAACACTACTATCGCAAAGCGATTTTC-AAATTCGT
* * * * *
49061 AACGCTAATTACCGACATAGGGAAATACTACTATCGCAACA-CGATTTTTAAATTCGC
1 AACGCTAATTACCGATATAGGTAAACACTACTATCGCAA-AGCGATTTTCAAATTCGT
49118 AACG
1 AACG
49122 TTATTTTCAC
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
57 57 0.53
58 49 0.46
59 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (57 bp):
AACGCTAATTACCGATATAGGTAAACACTACTATCGCAAAGCGATTTTCAAATTCGT
Found at i:49423 original size:20 final size:20
Alignment explanation
Indices: 49398--49467 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
49388 TCGGTAATTA
* *
49398 GCGTTGCAATTTTACTATTC
1 GCGTTGCGATTTTCCTATTC
49418 GCGTTGCGATTTTCCTATTC
1 GCGTTGCGATTTTCCTATTC
* *
49438 GAGTTTCGATTTTCCTATTC
1 GCGTTGCGATTTTCCTATTC
49458 GCGTTGCGAT
1 GCGTTGCGAT
49468 ATTACTGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (20 bp):
GCGTTGCGATTTTCCTATTC
Found at i:49436 original size:77 final size:77
Alignment explanation
Indices: 49302--49447 Score: 195
Period size: 77 Copynumber: 1.9 Consensus size: 77
49292 TTTCGATTGT
*
49302 TTACCTATATCGGTAATTAGCATTGCGAATTTGAAAATCGCGTTGCGATTAAACTATTCGCGTTG
1 TTACCTATATCGGTAATTAGCATTGCGAATTTGAAAATCGCGTTGCGATTAAACTATTCGAGTTG
49367 CGATAGTACTGG
66 CGATAGTACTGG
* * * * ***
49379 TTACCTATATCGGTAATTAGCGTTGC-AATTTTACTATTCGCGTTGCGATTTTCCTATTCGAGTT
1 TTACCTATATCGGTAATTAGCATTGCGAATTTGA-AAATCGCGTTGCGATTAAACTATTCGAGTT
*
49443 TCGAT
65 GCGAT
49448 TTTCCTATTC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
76 6 0.10
77 53 0.90
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (77 bp):
TTACCTATATCGGTAATTAGCATTGCGAATTTGAAAATCGCGTTGCGATTAAACTATTCGAGTTG
CGATAGTACTGG
Found at i:53875 original size:41 final size:41
Alignment explanation
Indices: 53830--53913 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
53820 TTTTCTGAAA
* *
53830 TTTCGTATTTGTTTCATGTAATT-TTTTTTTCGGAAAATATT
1 TTTCGTATTTGTTTCATGTAATTCGTTTTTT-GAAAAATATT
* *
53871 TTTCGTGTTTGTTTTATGTAATTCGTTTTTTGAAAAATATT
1 TTTCGTATTTGTTTCATGTAATTCGTTTTTTGAAAAATATT
53912 TT
1 TT
53914 CCCATGTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 32 0.84
42 6 0.16
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (41 bp):
TTTCGTATTTGTTTCATGTAATTCGTTTTTTGAAAAATATT
Found at i:55682 original size:14 final size:14
Alignment explanation
Indices: 55663--55695 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
55653 CCGAGAGCAT
55663 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
55677 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
55691 ACGAG
1 CCGAG
55696 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:55716 original size:10 final size:10
Alignment explanation
Indices: 55701--55757 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
55691 ACGAGCTATG
55701 CGAGGGCATC
1 CGAGGGCATC
*
55711 CGAGGGCAAC
1 CGAGGGCATC
*
55721 CGAGCGAGCTATA
1 CGAG-G-GC-ATC
*
55734 CGAGGGAATC
1 CGAGGGCATC
*
55744 CGAGGGCAAC
1 CGAGGGCATC
55754 CGAG
1 CGAG
55758 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.28, C:0.26, G:0.39, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:55729 original size:33 final size:33
Alignment explanation
Indices: 55677--55761 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
55667 GGCCATCCGA
* * * * *
55677 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATACGAGGGAAT
55710 CCGAGGGCAACCGAGCGAGCTATACGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATACGAGGGAAT
55743 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
55762 GGTAGGTCGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.36, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATACGAGGGAAT
Found at i:55837 original size:10 final size:10
Alignment explanation
Indices: 55822--55943 Score: 64
Period size: 10 Copynumber: 11.5 Consensus size: 10
55812 GGCGACCTTG
55822 TGCCCTCGGA
1 TGCCCTCGGA
*
55832 TGCCCTCGCA
1 TGCCCTCGGA
*
55842 TAGCTCGTTCGGA
1 T-GC-C-CTCGGA
55855 TGGCCTCGGTCGGA
1 T-GCC-C--TCGGA
*
55869 TGGCCTCGGA
1 TGCCCTCGGA
* *
55879 TGCTCTCAGA
1 TGCCCTCGGA
*
55889 TGGCCTCGGA
1 TGCCCTCGGA
**
55899 TGCTTTCGGA
1 TGCCCTCGGA
*
55909 TGGCCTCGGA
1 TGCCCTCGGA
**
55919 TGCTTTCGGA
1 TGCCCTCGGA
* *
55929 TGGCCTCAGA
1 TGCCCTCGGA
55939 TGCCC
1 TGCCC
55944 AGCGTGTTGG
Statistics
Matches: 80, Mismatches: 27, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
10 60 0.75
11 2 0.03
12 3 0.04
13 9 0.11
14 6 0.08
ACGTcount: A:0.11, C:0.31, G:0.32, T:0.25
Consensus pattern (10 bp):
TGCCCTCGGA
Found at i:55867 original size:14 final size:14
Alignment explanation
Indices: 55845--55877 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
55835 CCTCGCATAG
*
55845 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
55859 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
55873 CTCGG
1 CTCGG
55878 ATGCTCTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:55892 original size:20 final size:20
Alignment explanation
Indices: 55864--55941 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
55854 ATGGCCTCGG
*
55864 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTT
*
55884 TCAGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTT
55904 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTT
*
55924 TCGGATGGCCTCAGATGC
1 TCGGATGGCCTCGGATGC
55942 CCAGCGTGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTT
Found at i:56013 original size:29 final size:29
Alignment explanation
Indices: 55980--56037 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
55970 GCAATCTCTT
*
55980 GTAGGTCGCCGGGAAGACATGGCGACCTA
1 GTAGGTCGCCCGGAAGACATGGCGACCTA
**
56009 GTAGGTCGCCCGGAAGGTATGGCGACCTA
1 GTAGGTCGCCCGGAAGACATGGCGACCTA
56038 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (29 bp):
GTAGGTCGCCCGGAAGACATGGCGACCTA
Found at i:58192 original size:2 final size:2
Alignment explanation
Indices: 58185--58225 Score: 55
Period size: 2 Copynumber: 19.0 Consensus size: 2
58175 ATGAACATGG
58185 AT AT AT AT AT AT AT AT AGT AT AT AGT AT AT AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT
58226 GTATGAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 30 0.83
3 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:58208 original size:7 final size:7
Alignment explanation
Indices: 58185--58222 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
58175 ATGAACATGG
58185 ATATA-T
1 ATATAGT
58191 ATATA-T
1 ATATAGT
58197 ATATAGT
1 ATATAGT
58204 ATATAGT
1 ATATAGT
58211 ATATAGT
1 ATATAGT
58218 ATATA
1 ATATA
58223 TATGTATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (7 bp):
ATATAGT
Found at i:61251 original size:22 final size:24
Alignment explanation
Indices: 61208--61262 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
61198 CCGAAATAAT
* *
61208 AATAAAAAT-ATTATTTTTATT-A
1 AATAAAAATAATGATTTTAATTAA
61230 AATAAAAATAATGA-TTTAATTAA
1 AATAAAAATAATGATTTTAATTAA
*
61253 AATAATAATA
1 AATAAAAATA
61263 TATATATAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AATAAAAATAATGATTTTAATTAA
Found at i:68806 original size:16 final size:16
Alignment explanation
Indices: 68785--68825 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
68775 GTTTTGTTGT
68785 TTCATTCAGCATAGTC
1 TTCATTCAGCATAGTC
*
68801 TTCATTCAGCATTGTC
1 TTCATTCAGCATAGTC
68817 TTCATTCAG
1 TTCATTCAG
68826 AGGTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.41
Consensus pattern (16 bp):
TTCATTCAGCATAGTC
Found at i:70300 original size:59 final size:59
Alignment explanation
Indices: 70235--70382 Score: 269
Period size: 59 Copynumber: 2.5 Consensus size: 59
70225 GACTATTTTA
70235 TAACTTTTAATAGTCGGGGGACTCAACAAAGTAACGCCCTATAGTCGGAGATTATTGTG
1 TAACTTTTAATAGTCGGGGGACTCAACAAAGTAACGCCCTATAGTCGGAGATTATTGTG
* *
70294 TAACTTTTAATAGTCAGGGGACTTAACAAAGTAACGCCCTATAGTCGGAGATTATTGTG
1 TAACTTTTAATAGTCGGGGGACTCAACAAAGTAACGCCCTATAGTCGGAGATTATTGTG
*
70353 TAACTTTTAATAGTCGAGGGACTCAACAAA
1 TAACTTTTAATAGTCGGGGGACTCAACAAA
70383 ACGATGCCCT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 84 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (59 bp):
TAACTTTTAATAGTCGGGGGACTCAACAAAGTAACGCCCTATAGTCGGAGATTATTGTG
Found at i:70306 original size:28 final size:28
Alignment explanation
Indices: 70275--70368 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 28
70265 GTAACGCCCT
70275 ATAGTCGGAGATTATTGTGTAACTTTTA
1 ATAGTCGGAGATTATTGTGTAACTTTTA
* **** ***
70303 ATAGTCAGGGGACTTAACAAAGTAACGCCCT-
1 ATAGTC-GGAGA-TT-ATTGTGTAAC-TTTTA
70334 ATAGTCGGAGATTATTGTGTAACTTTTA
1 ATAGTCGGAGATTATTGTGTAACTTTTA
70362 ATAGTCG
1 ATAGTCG
70369 AGGGACTCAA
Statistics
Matches: 45, Mismatches: 16, Indels: 10
0.63 0.23 0.14
Matches are distributed among these distances:
27 1 0.02
28 19 0.42
29 6 0.13
30 6 0.13
31 12 0.27
32 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (28 bp):
ATAGTCGGAGATTATTGTGTAACTTTTA
Found at i:74001 original size:19 final size:21
Alignment explanation
Indices: 73974--74012 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
73964 TGAAAGACGT
73974 AAATAAATATTAAT-ATTTTA
1 AAATAAATATTAATAATTTTA
73994 AAAT-AATATTAATAATTTT
1 AAATAAATATTAATAATTTT
74013 GTTAAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAAATATTAATAATTTTA
Found at i:74656 original size:26 final size:26
Alignment explanation
Indices: 74528--74643 Score: 205
Period size: 26 Copynumber: 4.5 Consensus size: 26
74518 AAGAGCTTAG
*
74528 AGGGAGAGAAGTGATCCTTGTTATGT
1 AGGGAGAAAAGTGATCCTTGTTATGT
*
74554 AGGGAGAAAAGTGACCCTTGTTATGT
1 AGGGAGAAAAGTGATCCTTGTTATGT
74580 AGGGAGAAAAGTGATCCTTGTTATGT
1 AGGGAGAAAAGTGATCCTTGTTATGT
74606 AGGGAGAAAAGTGATCCTTGTTATGT
1 AGGGAGAAAAGTGATCCTTGTTATGT
*
74632 AGGGATAAAAGT
1 AGGGAGAAAAGT
74644 TGTACCTAGT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 86 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (26 bp):
AGGGAGAAAAGTGATCCTTGTTATGT
Found at i:75897 original size:77 final size:80
Alignment explanation
Indices: 75802--75961 Score: 229
Period size: 77 Copynumber: 2.0 Consensus size: 80
75792 AAAACAATTC
* * *
75802 ACTATATAATAGAGAAGTTTAGAACTATTGTAGG-GGGCCATATGAAATGAAATCAC-TGAGAGG
1 ACTATATAATAGAGAAGTTTAGAACTATTATAGGAGGCCCATATGAAATGAAAACACTTGAGAGG
75865 GAC-AAGTTAAAAAA
66 GACAAAGTTAAAAAA
*
75879 ACTAT-TATATAGAGAAGTTTAGAATTATTATAGGAGGCCCATATGAAATGAAAACACTTGAGAG
1 ACTATATA-ATAGAGAAGTTTAGAACTATTATAGGAGGCCCATATGAAATGAAAACACTTGAGAG
* *
75943 GGTCAAAGTTAAAGAA
65 GGACAAAGTTAAAAAA
75959 ACT
1 ACT
75962 TGTTTGAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
76 2 0.03
77 29 0.40
78 20 0.27
79 9 0.12
80 13 0.18
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (80 bp):
ACTATATAATAGAGAAGTTTAGAACTATTATAGGAGGCCCATATGAAATGAAAACACTTGAGAGG
GACAAAGTTAAAAAA
Found at i:76656 original size:21 final size:21
Alignment explanation
Indices: 76632--76673 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
76622 TGTTAATTTA
76632 ATTAAAAATATAA-ATATTTTT
1 ATTAAAAATATAATA-ATTTTT
*
76653 ATTAATAATATAATAATTTTT
1 ATTAAAAATATAATAATTTTT
76674 TATCCTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAAAAATATAATAATTTTT
Found at i:77297 original size:21 final size:21
Alignment explanation
Indices: 77271--77322 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
77261 ACGTTAAAAG
*
77271 ATTAACATTTTAGATAACGAA
1 ATTAACATTTTAGATAACAAA
77292 ATTAACATTTTAGATAACAAA
1 ATTAACATTTTAGATAACAAA
77313 ATTAACATTT
1 ATTAACATTT
77323 AGGTAGCACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (21 bp):
ATTAACATTTTAGATAACAAA
Found at i:79885 original size:41 final size:39
Alignment explanation
Indices: 79825--79904 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 39
79815 GCCATAGTAC
*
79825 AATGAGCTTAAGGACGAGAATGAGATGGAATTTAGAGAGTT
1 AATGAGCTTAAGGACGAGAATGAGA--GAATTTAAAGAGTT
** *
79866 AATGAGCTTGGGGATGAGAATGAGAGAATTTAAAGAGTT
1 AATGAGCTTAAGGACGAGAATGAGAGAATTTAAAGAGTT
79905 TGAGATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 13 0.37
41 22 0.63
ACGTcount: A:0.39, C:0.04, G:0.33, T:0.25
Consensus pattern (39 bp):
AATGAGCTTAAGGACGAGAATGAGAGAATTTAAAGAGTT
Found at i:80231 original size:41 final size:39
Alignment explanation
Indices: 80171--80250 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 39
80161 ATATCTGTAC
*
80171 AATGAGCTTAAGGACGAGAATGAGATGGAATTTAGAGAGTT
1 AATGAGCTTAAGGACGAGAATGAGA--GAATTTAAAGAGTT
** *
80212 AATGAGCTTGGGGATGAGAATGAGAGAATTTAAAGAGTT
1 AATGAGCTTAAGGACGAGAATGAGAGAATTTAAAGAGTT
80251 TGAGATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 13 0.37
41 22 0.63
ACGTcount: A:0.39, C:0.04, G:0.33, T:0.25
Consensus pattern (39 bp):
AATGAGCTTAAGGACGAGAATGAGAGAATTTAAAGAGTT
Found at i:80255 original size:346 final size:332
Alignment explanation
Indices: 79580--80260 Score: 1227
Period size: 346 Copynumber: 2.0 Consensus size: 332
79570 TTTAAACCCC
79580 AAAAGATGTTTTGAATCATAAACTTATGATCTGAGACGACTCTTTAATCCCATAAGTAATCGGTT
1 AAAAGATGTTTTGAATCATAAACTTATGATCTGAGACGACTCTTTAATCCCATAAGTAATCGGTT
79645 TTGAACGCGATATGTTTTCATCGATCACTGAATTTGGTCCCTCGGCACGCTCGATAACGTCCCCT
66 TTGAACGCGATATGTTTTCATCGATCACTGAATTTGGTCCCTCGGCACGCTCGATAACGTCCCCT
79710 GCAGGGCTCAACACATTGTCGGCGGAGGCTTTGATTTTCTGTCGTCTCCTACCACAACCGGGTCG
131 GCAGGGCTCAACACATTGTCGGCGGAGGCTTTGATTTTCTGTCGTCTCCTACCACAACCGGGTCG
*
79775 AAAGAATCACGACGAGTGAGAATACCCAAAAGCAATCTTCGCCATAGTACAATGAGCTTAAGGAC
196 AAAGAATCACGACGAGTGAGAATACACAAAAGCAATCTTCGCCATAGTACAATGAGCTTAAGGAC
79840 GAGAATGAGATGGAATTTAGAGAGTTAATGAGCTTGGGGATGAGAATGAGAGAATTTAAAGAGTT
261 GAGAATGAGATGGAATTTAGAGAGTTAATGAGCTTGGGGATGAGAATGAGAGAATTTAAAGAGTT
79905 TGAGATG
326 TGAGATG
79912 AAAAGATGTTTTGAATCATAAACTTATGGATTGATCTGAGACGACTCTTTAATCCCATAAGTAAT
1 AAAAGATGTTTTGAATCATAAAC-T-T--A-TGATCTGAGACGACTCTTTAATCCCATAAGTAAT
79977 CGGTTTTGAACGCGAATATGGTTCTTCATCGATCACTGAATTTGGTCCCTCGGCACGCTCGATAA
61 CGGTTTTGAACGCG-ATAT-GTT-TTCATCGATCACTGAATTTGGTCCCTCGGCACGCTCGATAA
80042 CGTCCCCTGCAGGGCTCAACACATTGTCGGCGGAGGCTTTGATTTTCTTGTCGTCTCCTACCACA
123 CGTCCCCTGCAGGGCTCAACACATTGTCGGCGGAGGCTTTGATTTTC-TGTCGTCTCCTACCAC-
80107 AACCGGGTCGAAAGAATCACGACGAGTGAGAATACAACAAAAGCAATCTTCGCCATATCTGTACA
186 AACCGGGTCGAAAGAATCACGACGAGTGAGAATAC-ACAAAAGCAATCTTCGCCATA---GTACA
80172 ATGAGCTTAAGGACGAGAATGAGATGGAATTTAGAGAGTTAATGAGCTTGGGGATGAGAATGAGA
247 ATGAGCTTAAGGACGAGAATGAGATGGAATTTAGAGAGTTAATGAGCTTGGGGATGAGAATGAGA
80237 GAATTTAAAGAGTTTGAGATG
312 GAATTTAAAGAGTTTGAGATG
80258 AAA
1 AAA
80261 TATTTACGAT
Statistics
Matches: 334, Mismatches: 1, Indels: 14
0.96 0.00 0.04
Matches are distributed among these distances:
332 23 0.07
333 1 0.00
334 1 0.00
336 1 0.00
337 48 0.14
338 4 0.01
339 3 0.01
340 88 0.26
341 16 0.05
342 35 0.10
343 20 0.06
346 94 0.28
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (332 bp):
AAAAGATGTTTTGAATCATAAACTTATGATCTGAGACGACTCTTTAATCCCATAAGTAATCGGTT
TTGAACGCGATATGTTTTCATCGATCACTGAATTTGGTCCCTCGGCACGCTCGATAACGTCCCCT
GCAGGGCTCAACACATTGTCGGCGGAGGCTTTGATTTTCTGTCGTCTCCTACCACAACCGGGTCG
AAAGAATCACGACGAGTGAGAATACACAAAAGCAATCTTCGCCATAGTACAATGAGCTTAAGGAC
GAGAATGAGATGGAATTTAGAGAGTTAATGAGCTTGGGGATGAGAATGAGAGAATTTAAAGAGTT
TGAGATG
Found at i:80684 original size:2 final size:2
Alignment explanation
Indices: 80677--80709 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
80667 ATCTTTTCTC
80677 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 A
80710 AATGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83746 original size:94 final size:94
Alignment explanation
Indices: 83585--83773 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
83575 AACTTTGGTG
83585 GGATATTTATACTCCCTCCGTCGATGGTCATTTTCGATCCTAACAGAGGTTGTTTTCCTCGTCCC
1 GGATATTTATACTCCCTCCGTCGATGGTCATTTTCGATCCTAACAGAGGTTGTTTTCCTCGTCCC
83650 CATTTTACTATGGCCGATTTATTATTAGT
66 CATTTTACTATGGCCGATTTATTATTAGT
83679 GGATATTTATACTCCCTCCGTCGATGGTCATTTTCGATCCTAACAGAGGTTGTTTTCCTCGTCCC
1 GGATATTTATACTCCCTCCGTCGATGGTCATTTTCGATCCTAACAGAGGTTGTTTTCCTCGTCCC
83744 CATTTTACTATGGCCGATTTATTATTAGT
66 CATTTTACTATGGCCGATTTATTATTAGT
83773 G
1 G
83774 TTGGTCGGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (94 bp):
GGATATTTATACTCCCTCCGTCGATGGTCATTTTCGATCCTAACAGAGGTTGTTTTCCTCGTCCC
CATTTTACTATGGCCGATTTATTATTAGT
Found at i:84126 original size:5 final size:5
Alignment explanation
Indices: 84035--84503 Score: 485
Period size: 5 Copynumber: 96.6 Consensus size: 5
84025 ACCTGAATGA
84035 AATA- AATA- AATAGT AA-AT AA-AT AATAT AAATAT AA-A- AATAAT
1 AATAT AATAT AATA-T AATAT AATAT AATAT -AATAT AATAT AAT-AT
* * * * *
84077 TATAT AA-AT AATAT TATAC AATAT AAATAC AATACT CATAT -ATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATA-T AATAT AATAT AATAT
84127 AA-AT AATAT AATAT -ATAT -ATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
84174 AATAT -A-AT AATAT AATAT -A-AT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
84220 AATAT -A-AT AATAT AATAT AATAT AATAT AATAT AATATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -A-ATAT AATAT AATAT
84270 -A-AT AATAT AATAT -A-AT AATAT AATAAT ATATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AAT-AT A-ATAT AATAT AATAT AATAT
84318 -ATAT AATA- AATAT AATAT AATAT -ATA- ATATAT ATATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT A-ATAT AATAT AATAT
84366 AATAT -ATAT -ATAT AATAT AATAT ATATAT AATA- AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT
* * *
84414 AATAT AATAT AATAT AATAT AA-ATT AACAT AATAT AATAT AAATTT AACAT
1 AATAT AATAT AATAT AATAT AATA-T AATAT AATAT AATAT -AATAT AATAT
* * *
84465 AATATAT AATAT ATTAT AATAT ACTAT ACTAT -ATAT AAT
1 -A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
84504 TTACATATTT
Statistics
Matches: 406, Mismatches: 18, Indels: 81
0.80 0.04 0.16
Matches are distributed among these distances:
3 12 0.03
4 73 0.18
5 269 0.66
6 43 0.11
7 9 0.02
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:84275 original size:53 final size:52
Alignment explanation
Indices: 84072--84487 Score: 425
Period size: 53 Copynumber: 7.9 Consensus size: 52
84062 AAATATAAAA
* * * * *
84072 ATAATTATATAA-ATAATATTATACAATATAAATACAATACTCATATATATAAT
1 ATAATAATATAATATAATATAATATAATATAAATATAATA-TAATATA-ATAAT
84125 ATAAATAATATAATAT-ATAT-ATATAATAT-AATATAATATAATATAATATAAT
1 AT-AATAATATAATATAATATAATATAATATAAATATAATATAATAT-A-ATAAT
84177 ATAATAATATAATAT-A-ATAATATAATAT-AATATAATATAATATAAT-AT
1 ATAATAATATAATATAATATAATATAATATAAATATAATATAATATAATAAT
84225 AATAATATAATATAATATAATATAATATAATATATAATATAATATAATA-ATATAAT
1 -AT-A-ATAATATAATATAATATAATATAATATA-AATATAATATAATATA-ATAAT
*
84281 ATAATAATATAATAATATATATAATATAATAT-AATAT-ATATAATAAATATAAT
1 ATAATAATATAAT-ATA-ATATAATATAATATAAATATAATATAATATA-ATAAT
84334 ATAAT-ATATAATATATATATATAATATAATATAATATATATATATAATATAAT-AT
1 ATAATAATAT-A-ATATA-ATATAATATAATATAA-ATATA-ATATAATATAATAAT
*
84389 ATATATAATA-AATATAATATAATATAATAT-AATATAATATAATATAA-ATT
1 ATA-ATAATATAATATAATATAATATAATATAAATATAATATAATATAATAAT
* * *
84439 A-ACATAATATAATATAAATTTAACATAATATATAATATATTATAATATA
1 ATA-ATAATATAATAT-AATATAATATAATATA-AATATAATATAATATA
84488 CTATACTATA
Statistics
Matches: 324, Mismatches: 10, Indels: 58
0.83 0.03 0.15
Matches are distributed among these distances:
48 2 0.01
49 11 0.03
50 22 0.07
51 73 0.23
52 31 0.10
53 97 0.30
54 26 0.08
55 44 0.14
56 6 0.02
57 12 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (52 bp):
ATAATAATATAATATAATATAATATAATATAAATATAATATAATATAATAAT
Found at i:92298 original size:2 final size:2
Alignment explanation
Indices: 92291--92321 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
92281 GTTCACATGA
92291 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 A
92322 AAGCAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95743 original size:60 final size:60
Alignment explanation
Indices: 95664--95778 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
95654 CAAAAGTAAT
* * *
95664 AAATTGATCACTAAAACATCAAATA-GATCATTGAACAATGATTTTATATCTAATTCTAAA
1 AAATTGATCACCAAAACATCAAATATGATC-TGGAACAATAATTTTATATCTAATTCTAAA
* *
95724 AAATTGGTCACCAAAACATCAAATATGTTCTGGAACAATAATTTTATATCTAATT
1 AAATTGATCACCAAAACATCAAATATGATCTGGAACAATAATTTTATATCTAATT
95779 TATTCTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 46 0.94
61 3 0.06
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (60 bp):
AAATTGATCACCAAAACATCAAATATGATCTGGAACAATAATTTTATATCTAATTCTAAA
Found at i:96043 original size:31 final size:32
Alignment explanation
Indices: 96005--96068 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
95995 TAATCATGTC
* *
96005 TTAATTAAATAAAAGTCAAAGTGA-TAAATAT
1 TTAATTAAATAAAAATCAAAGTGACAAAATAT
*
96036 TTAATTAAATAAAAATGAAAGTGACAAAATAT
1 TTAATTAAATAAAAATCAAAGTGACAAAATAT
96068 T
1 T
96069 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.31
Consensus pattern (32 bp):
TTAATTAAATAAAAATCAAAGTGACAAAATAT
Found at i:98028 original size:43 final size:42
Alignment explanation
Indices: 97978--98251 Score: 201
Period size: 43 Copynumber: 6.4 Consensus size: 42
97968 TGGTAACAAA
* ** * **
97978 AAACGCCGCAACAGGTAACGATATATAGCGGCGTTTGTTGGAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTT-TTCAAC
* *
98021 AAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTTT-CAAC
* * *
98064 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCG-TTTTTCAAC
* * *
98107 AAACGCCGCAATAGGTATTGAGATTTAGCAGCGTTTTTTACAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTTTCA-AC
* ** * * * * * *
98150 AAACACCGCAATATATCTTGAGATTTTGCAGCATTTTTCCCAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTTT-CAAC
* * * * *
98193 AAACGCCGCAA-AAG-ATCTGGTATATAGCTGCGTTTTTTAGAAC
1 AAACGCCGCAATAGGTAT-TGATATTTAGCGGCG-TTTTT-CAAC
*
98236 AAACGCCGCAAAAGGT
1 AAACGCCGCAATAGGT
98252 TATATCTATA
Statistics
Matches: 186, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
41 1 0.01
42 17 0.09
43 161 0.87
44 7 0.04
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (42 bp):
AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTTTCAAC
Found at i:98093 original size:86 final size:86
Alignment explanation
Indices: 98003--98203 Score: 235
Period size: 86 Copynumber: 2.3 Consensus size: 86
97993 TAACGATATA
** * * * *
98003 TAGCGGCGTTTGTTGGACAAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTC-CAACAAA
1 TAGCGGCGTTTGTTCCACAAACGCCGCAATAGGTATTGAGATTTAGCAGCGTTTTTCAC-ACAAA
*
98067 CGCCGCAATAGGTGTTGAGATT
65 CACCGCAATAGGTGTTGAGATT
* *
98089 TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTATTGAGATTTAGCAGCGTTTTTTACACAAAC
1 TAGCGGCGTTTGTTCCACAAACGCCGCAATAGGTATTGAGATTTAGCAGCGTTTTTCACACAAAC
** *
98154 ACCGCAATATATCTTGAGATT
66 ACCGCAATAGGTGTTGAGATT
* * *
98175 TTGCAGCATTT-TTCCCACAAACGCCGCAA
1 TAGCGGCGTTTGTT-CCACAAACGCCGCAA
98204 AAGATCTGGT
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 2 0.02
86 95 0.97
87 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (86 bp):
TAGCGGCGTTTGTTCCACAAACGCCGCAATAGGTATTGAGATTTAGCAGCGTTTTTCACACAAAC
ACCGCAATAGGTGTTGAGATT
Found at i:102140 original size:41 final size:41
Alignment explanation
Indices: 102084--102472 Score: 334
Period size: 41 Copynumber: 9.3 Consensus size: 41
102074 TTGTGTTTAC
* *
102084 AAACGCCACTAAAGTACAAGTCTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
102125 AAATGCCACTGAAGTACGAGTCTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
102166 AAACGCCACTGAAGTATGAGTCTATAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * * *
102207 AAATGCCACTGAATTACAAGTCTTTAGCAGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * *
102249 CAAACGCCACTAAAGTACGAGTCGTTAACGGCGTTTGTACAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
102291 AAACGCCACTAATGAACTCA-TTTTTAGCGGCGTTTGTACAAA
1 AAACGCCACTAAAGTAC-GAGTCTTTAGCGGCGTTTGTA-TAA
102333 AAATGCCGCTAACCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAA---CG----CCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
102381 AAACCCCACTAAATTAC-AATATTTAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * * *
102421 AAACTCTACTAAAATATGAGTATTTAGCGGCGTTT-TAAAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT-ATAA
*
102462 AAACTCCACTA
1 AAACGCCACTA
102473 TAGCACATGT
Statistics
Matches: 286, Mismatches: 48, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
40 34 0.12
41 176 0.62
42 8 0.03
43 32 0.11
45 3 0.01
48 6 0.02
49 27 0.09
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:102420 original size:40 final size:40
Alignment explanation
Indices: 102362--102472 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 40
102352 AGTACGAGTC
* *
102362 TTTAGCGGCGTTTGTATAAAAACCCCACTAAATTA-CAATA
1 TTTAGCGGCGTTT-TATAAAAACTCCACTAAAATATCAATA
* * *
102402 TTTAGCGGCGTTTATATAAAAACTCTACTAAAATATGAGTA
1 TTTAGCGGCGTTT-TATAAAAACTCCACTAAAATATCAATA
*
102443 TTTAGCGGCGTTTTAAAAAAAACTCCACTA
1 TTTAGCGGCGTTTT-ATAAAAACTCCACTA
102473 TAGCACATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 32 0.52
41 29 0.48
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (40 bp):
TTTAGCGGCGTTTTATAAAAACTCCACTAAAATATCAATA
Found at i:103071 original size:16 final size:16
Alignment explanation
Indices: 103025--103075 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
103015 TTCAGATTAT
*
103025 TTTTTG-TTCGAATTG
1 TTTTTGATTCGAGTTG
*
103040 TTTTTGGTTCGAGTTG
1 TTTTTGATTCGAGTTG
* *
103056 TTTTTTATTCGGGTTG
1 TTTTTGATTCGAGTTG
103072 TTTT
1 TTTT
103076 CGGTTCAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 6 0.19
16 25 0.81
ACGTcount: A:0.08, C:0.06, G:0.24, T:0.63
Consensus pattern (16 bp):
TTTTTGATTCGAGTTG
Found at i:104109 original size:12 final size:12
Alignment explanation
Indices: 104092--104117 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
104082 TAATTTGTCC
104092 GTGTAATTTAAG
1 GTGTAATTTAAG
104104 GTGTAATTTAAG
1 GTGTAATTTAAG
104116 GT
1 GT
104118 TAAAGAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (12 bp):
GTGTAATTTAAG
Found at i:107904 original size:2 final size:2
Alignment explanation
Indices: 107897--107932 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
107887 CTTGTGTATT
107897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
107933 GTGATATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109295 original size:14 final size:14
Alignment explanation
Indices: 109257--109297 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
109247 GGATTATTGT
*
109257 AAATTAAGAGAGTA
1 AAATTAAGAGGGTA
109271 AAATTAAGAGGGTA
1 AAATTAAGAGGGTA
109285 AAATTAAGAGGGT
1 AAATTAAGAGGGT
109298 CATTCTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (14 bp):
AAATTAAGAGGGTA
Found at i:110394 original size:6 final size:6
Alignment explanation
Indices: 110383--110408 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
110373 GTTAATATGC
110383 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
110409 TTGATTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:111438 original size:11 final size:10
Alignment explanation
Indices: 111415--111452 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
111405 TTTAAACTAA
*
111415 ATTAAAATAT
1 ATTAAATTAT
111425 ATTAATATTAT
1 ATTAA-ATTAT
111436 ATTAAATT-T
1 ATTAAATTAT
111445 ATTAAATT
1 ATTAAATT
111453 TACATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.35
10 8 0.31
11 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTAAATTAT
Found at i:112610 original size:21 final size:21
Alignment explanation
Indices: 112584--112623 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
112574 CCAGTTCTAA
*
112584 TGTTGTTTGTTTTCTTTTTGT
1 TGTTGTTGGTTTTCTTTTTGT
*
112605 TGTTGTTGGTTTTTTTTTT
1 TGTTGTTGGTTTTCTTTTT
112624 TTTGCTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.20, T:0.78
Consensus pattern (21 bp):
TGTTGTTGGTTTTCTTTTTGT
Found at i:118213 original size:31 final size:32
Alignment explanation
Indices: 118175--118247 Score: 139
Period size: 31 Copynumber: 2.3 Consensus size: 32
118165 TTAAGAGACT
118175 AAATAAGAATAGAGTACTTTTTTAGA-AAAAA
1 AAATAAGAATAGAGTACTTTTTTAGAGAAAAA
118206 AAATAAGAATAGAGTACTTTTTTAGAGAAAAA
1 AAATAAGAATAGAGTACTTTTTTAGAGAAAAA
118238 AAATAAGAAT
1 AAATAAGAAT
118248 TGAAATTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 26 0.63
32 15 0.37
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (32 bp):
AAATAAGAATAGAGTACTTTTTTAGAGAAAAA
Found at i:118966 original size:75 final size:75
Alignment explanation
Indices: 118809--119015 Score: 281
Period size: 75 Copynumber: 2.8 Consensus size: 75
118799 CAAAGTCAAA
* * * **
118809 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
118874 TTGGCTCCGAG
65 TTGGCTCCGAG
* *
118885 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAATCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
118950 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
118960 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCT
119016 TGTACAACGG
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
74 18 0.16
75 72 0.62
76 26 0.22
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:124953 original size:75 final size:77
Alignment explanation
Indices: 124765--124976 Score: 250
Period size: 77 Copynumber: 2.7 Consensus size: 77
124755 CAAAGCCAAA
* * * *
124765 AATTACAGATTGCTCAGAGGGAACCGATTTCCCCCCCCCATAGGAGGAACCGATT--CCCCCTGA
1 AATTCCAGAATGCTCGGAGGGAACCGA-TT---CCCCCCATAGGAGGAACCGATTCCCCCCCTAA
***
124828 ATGGTTTGGCTCCGAG
62 ACAATTTGGCTCCGAG
*
124844 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCCTAAACAA
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCCTAAACAA
*
124909 TTTTGCTCCGAG
66 TTTGGCTCCGAG
* * * *
124921 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCC
124977 TTGTACAACG
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
75 22 0.19
76 18 0.15
77 52 0.44
78 2 0.02
79 23 0.20
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCCTAAACAA
TTTGGCTCCGAG
Found at i:130792 original size:23 final size:21
Alignment explanation
Indices: 130740--130801 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
130730 TTTTGGTGCA
*
130740 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
130760 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
130781 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
130802 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:132759 original size:9 final size:8
Alignment explanation
Indices: 132738--132787 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
132728 TGTTTCAACA
132738 TTTGGATAT
1 TTTGGAT-T
132747 TTTGGATT
1 TTTGGATT
132755 GTTT-GATT
1 -TTTGGATT
132763 TTGTGGATT
1 TT-TGGATT
*
132772 GTTGGATT
1 TTTGGATT
132780 TTT-GATT
1 TTTGGATT
132787 T
1 T
132788 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 7 0.19
8 14 0.39
9 15 0.42
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (8 bp):
TTTGGATT
Found at i:132771 original size:17 final size:17
Alignment explanation
Indices: 132739--132781 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
132729 GTTTCAACAT
132739 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
132756 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
132773 TTGGATTTT
1 TTGGATTTT
132782 TGATTTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:133531 original size:76 final size:76
Alignment explanation
Indices: 133380--133591 Score: 273
Period size: 76 Copynumber: 2.8 Consensus size: 76
133370 CAAAGCCAAA
* * * * *
133380 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCCCATAGGAGGAACCGATTCCCCCCTGAAT
1 AATTCCAGAATGCTCGGAGGGAACCGATT---CCCCCCATAGGAGGAACCGATTCCCCCCTAAAC
*
133445 GGTTTGGCTCCGAG
63 AGTTTGGCTCCGAG
* *
133459 ATTTCCAGAATGCTCGGATGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
133524 TTTGCTCCGAG
66 TTGGCTCCGAG
* * * *
133535 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
133592 TGTACAACGG
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 19 0.16
76 75 0.64
79 24 0.20
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:136567 original size:9 final size:8
Alignment explanation
Indices: 136545--136595 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
136535 TGTTTCAACA
136545 TTTTGGAT
1 TTTTGGAT
136553 ATTTTGGAT
1 -TTTTGGAT
136562 TGTTT-GAT
1 T-TTTGGAT
136570 TTTGTGGAT
1 TTT-TGGAT
*
136579 TGTTGGA-
1 TTTTGGAT
136586 TTTTGGAT
1 TTTTGGAT
136594 TT
1 TT
136596 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:136579 original size:17 final size:17
Alignment explanation
Indices: 136547--136590 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
136537 TTTCAACATT
136547 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
136564 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
136581 TTGGATTTTG
1 TTGGATTTTG
136591 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:137320 original size:75 final size:75
Alignment explanation
Indices: 137169--137376 Score: 276
Period size: 75 Copynumber: 2.8 Consensus size: 75
137159 CAAAGTCAAA
* * * **
137169 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
137234 TTGGCTCCGAG
65 TTGGCTCCGAG
*
137245 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
137310 TTGTTCCGAG
66 TGGCTCCGAG
* * *
137320 AATTCCAGTATGCTCGGAGGGAATCGATCCCCCCCA-AGG-GGATACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGA-ACCGATTCCCCCCT
137377 TGTACAACGG
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
74 3 0.03
75 83 0.70
76 32 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:138523 original size:33 final size:34
Alignment explanation
Indices: 138485--138568 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
138475 CCCGAACCCG
138485 AAAATATTATATATATAATTAATATAAAA-AAAT
1 AAAATATTATATATATAATTAATATAAAATAAAT
*
138518 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAATAAAT
138552 AAAATATTATATATATA
1 AAAATATTATATATATA
138569 TATATATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 29 0.59
34 20 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAATAAAT
Found at i:140649 original size:31 final size:30
Alignment explanation
Indices: 140611--140684 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
140601 TTCTACCAAA
* *
140611 ATTTCAGCATTTCATCCC-CTTTAACTCTGTC
1 ATTTCAGC-TTTCATCCCTC-CTAACTCTGCC
140642 ATTTCAGCCTTTCATCCCTCCTAACTCTGCC
1 ATTTCAG-CTTTCATCCCTCCTAACTCTGCC
*
140673 ATGTCAGCTTTC
1 ATTTCAGCTTTC
140685 TGCGGGCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 5 0.13
31 31 0.82
32 2 0.05
ACGTcount: A:0.18, C:0.35, G:0.08, T:0.39
Consensus pattern (30 bp):
ATTTCAGCTTTCATCCCTCCTAACTCTGCC
Found at i:144753 original size:134 final size:135
Alignment explanation
Indices: 144546--144816 Score: 436
Period size: 134 Copynumber: 2.0 Consensus size: 135
144536 GGGGGGGGAA
* *
144546 CAGAAATCAGAAGGCAAAACAAGTTTGAGAAAAAAAATTAATTCTACCCAGAGATCTAATTCACA
1 CAGAAATCAGAAGGCAAAACAAGTTTCAGAAAAAAAATGAATTCTACCCAGAGATCTAATTCACA
* *
144611 TAAGAGTAAACAAATTCACAGCACCAAAGAGGCTAAGAACTAAAAGAATGGACCTTTAGGAAACA
66 TAAAAGTAAACAAATTCACACCACCAAAGAGGCTAAGAACTAAAAGAATGGACCTTTAGGAAACA
144676 AAACC
131 AAACC
* **
144681 CAGAAATCATAAGGCAAAACAAGTTTCAG-GGAAAAATGAATTCTACCCAGAGATCTAATTCACA
1 CAGAAATCAGAAGGCAAAACAAGTTTCAGAAAAAAAATGAATTCTACCCAGAGATCTAATTCACA
* * * *
144745 TAAAAGTAAACAAATTCACACCCCCAATGAGGCTAAGGACTAAAAGAATGGACTTTTAGGAAACA
66 TAAAAGTAAACAAATTCACACCACCAAAGAGGCTAAGAACTAAAAGAATGGACCTTTAGGAAACA
144810 AAACC
131 AAACC
144815 CA
1 CA
144817 ACAAGATGAA
Statistics
Matches: 125, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
134 98 0.78
135 27 0.22
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (135 bp):
CAGAAATCAGAAGGCAAAACAAGTTTCAGAAAAAAAATGAATTCTACCCAGAGATCTAATTCACA
TAAAAGTAAACAAATTCACACCACCAAAGAGGCTAAGAACTAAAAGAATGGACCTTTAGGAAACA
AAACC
Found at i:146204 original size:25 final size:25
Alignment explanation
Indices: 146175--146224 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
146165 ACATTTCGTA
146175 AACCAAACGCA-CTCTAATACATATG
1 AACCAAACGCACCT-TAATACATATG
*
146200 AACCAAATGCACCTTAATACATATG
1 AACCAAACGCACCTTAATACATATG
146225 CATCAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.22
Consensus pattern (25 bp):
AACCAAACGCACCTTAATACATATG
Found at i:148679 original size:54 final size:54
Alignment explanation
Indices: 148587--148691 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
148577 AAATTGAGAG
* * *
148587 TATATTTTATGAGTTTATCAAATCATAAGTGGAATGATAAATGATTTATATGAA
1 TATATTTTATGAATTTATCAAATCACAAGTAGAATGATAAATGATTTATATGAA
* *
148641 TATATTTTCTGAATTTATCAAATCACAAGTAGAGTGATAAATGATTTATAT
1 TATATTTTATGAATTTATCAAATCACAAGTAGAATGATAAATGATTTATAT
148692 TTAGTCTTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (54 bp):
TATATTTTATGAATTTATCAAATCACAAGTAGAATGATAAATGATTTATATGAA
Found at i:149362 original size:2 final size:2
Alignment explanation
Indices: 149355--149381 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
149345 TCGGTTCGTG
149355 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 A
149382 GTGTGTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:150523 original size:31 final size:32
Alignment explanation
Indices: 150488--150553 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
150478 CGAAAAATTC
150488 TTTAGGCACTAAAAATTAAC-TTTAAGTATAG
1 TTTAGGCACTAAAAATTAACTTTTAAGTATAG
*
150519 TTTAGTCACTAAAAATTAACTTTTAAGTATAG
1 TTTAGGCACTAAAAATTAACTTTTAAGTATAG
150551 TTT
1 TTT
150554 TTGCATGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (32 bp):
TTTAGGCACTAAAAATTAACTTTTAAGTATAG
Found at i:151115 original size:21 final size:21
Alignment explanation
Indices: 151089--151130 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
151079 TTTAGGGTTA
151089 GGGATTTTAGGA-TTTTTTTTT
1 GGGA-TTTAGGACTTTTTTTTT
*
151110 GGGATTTGGGACTTTTTTTTT
1 GGGATTTAGGACTTTTTTTTT
151131 ATAATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.12, C:0.02, G:0.26, T:0.60
Consensus pattern (21 bp):
GGGATTTAGGACTTTTTTTTT
Found at i:152053 original size:69 final size:69
Alignment explanation
Indices: 151942--152077 Score: 272
Period size: 69 Copynumber: 2.0 Consensus size: 69
151932 CATACATCCG
151942 TCATAGCATAAAGTCCATACACTATCTTCCCTTAAAAAATTACTAATATATTGATTATATTTTTT
1 TCATAGCATAAAGTCCATACACTATCTTCCCTTAAAAAATTACTAATATATTGATTATATTTTTT
152007 TGAA
66 TGAA
152011 TCATAGCATAAAGTCCATACACTATCTTCCCTTAAAAAATTACTAATATATTGATTATATTTTTT
1 TCATAGCATAAAGTCCATACACTATCTTCCCTTAAAAAATTACTAATATATTGATTATATTTTTT
152076 TG
66 TG
152078 GAAAAAAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (69 bp):
TCATAGCATAAAGTCCATACACTATCTTCCCTTAAAAAATTACTAATATATTGATTATATTTTTT
TGAA
Found at i:152665 original size:18 final size:20
Alignment explanation
Indices: 152644--152687 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
152634 AAAAAGAGAG
152644 AAATCAATC-AATC-ATAAA
1 AAATCAATCAAATCAATAAA
152662 AAATCAATCAAATCAAATAAA
1 AAATCAATCAAATC-AATAAA
152683 AAATC
1 AAATC
152688 CGAAGCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.39
19 4 0.17
21 10 0.43
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATCAATCAAATCAATAAA
Found at i:154705 original size:19 final size:19
Alignment explanation
Indices: 154681--154730 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
154671 AATTTTACAT
154681 ATATAAAAAAAT-CAGAAAA
1 ATATAAAAAAATCCA-AAAA
154700 ATATAAAAAAATCCAAAAA
1 ATATAAAAAAATCCAAAAA
154719 AT-TACAAAAAAT
1 ATATA-AAAAAAT
154731 AGTATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.07
19 25 0.86
20 2 0.07
ACGTcount: A:0.72, C:0.08, G:0.02, T:0.18
Consensus pattern (19 bp):
ATATAAAAAAATCCAAAAA
Found at i:154760 original size:11 final size:10
Alignment explanation
Indices: 154741--154771 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
154731 AGTATAATTA
154741 TTTATATATT
1 TTTATATATT
154751 TTTAATATATT
1 TTT-ATATATT
154762 TTTATATATT
1 TTTATATATT
154772 ATATAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATATATT
Found at i:154785 original size:17 final size:17
Alignment explanation
Indices: 154755--154788 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
154745 TATATTTTTA
* *
154755 ATATATTTTTATATATT
1 ATATAATTTAATATATT
154772 ATATAATTTAATATATT
1 ATATAATTTAATATATT
154789 TTAACCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATAATTTAATATATT
Found at i:155269 original size:17 final size:18
Alignment explanation
Indices: 155249--155284 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
155239 ATATAATAAG
*
155249 AGAAAAT-AATTTAAAAA
1 AGAAAATGAAATTAAAAA
155266 AGAAAATGAAATTAAAAA
1 AGAAAATGAAATTAAAAA
155284 A
1 A
155285 AAACAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (18 bp):
AGAAAATGAAATTAAAAA
Found at i:156364 original size:2 final size:2
Alignment explanation
Indices: 156357--156388 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
156347 CTATTTTTGA
156357 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
156389 TGTATAGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.