Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 57 of 125
Found at i:17476473 original size:9 final size:9
Alignment explanation
Indices: 17476459--17476537 Score: 51
Period size: 9 Copynumber: 10.3 Consensus size: 9
17476449 AAGGATGATG
17476459 ATTTTAATA
1 ATTTTAATA
17476468 ATTTT-AT-
1 ATTTTAATA
17476475 ATTTTAA-A
1 ATTTTAATA
17476483 A----AATA
1 ATTTTAATA
17476488 ATTTTAATA
1 ATTTTAATA
17476497 ATTTT-ATA
1 ATTTTAATA
*
17476505 TTTTTAA-A
1 ATTTTAATA
17476513 A----AATA
1 ATTTTAATA
17476518 ATTTTAATA
1 ATTTTAATA
17476527 ATTTTAA-A
1 ATTTTAATA
17476535 ATT
1 ATT
17476538 ATTTGTTGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 27
0.65 0.02 0.32
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
7 5 0.09
8 16 0.29
9 26 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTTTAATA
Found at i:17476480 original size:16 final size:16
Alignment explanation
Indices: 17476459--17476508 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
17476449 AAGGATGATG
17476459 ATTTTAATAATTTTAT
1 ATTTTAATAATTTTAT
**
17476475 ATTTTAA-AA-AATA-
1 ATTTTAATAATTTTAT
17476488 ATTTTAATAATTTTAT
1 ATTTTAATAATTTTAT
17476504 ATTTT
1 ATTTT
17476509 TAAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTAATAATTTTAT
Found at i:17476501 original size:29 final size:30
Alignment explanation
Indices: 17476459--17476532 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
17476449 AAGGATGATG
17476459 ATTTTAATAATTTTATA-TTTTAAAAAATA
1 ATTTTAATAATTTTATATTTTTAAAAAATA
17476488 ATTTTAATAATTTTATATTTTTAAAAAATA
1 ATTTTAATAATTTTATATTTTTAAAAAATA
17476518 ATTTTAATAATTTTA
1 ATTTTAATAATTTTA
17476533 AAATTATTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 17 0.39
30 27 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTTTAATAATTTTATATTTTTAAAAAATA
Found at i:17476519 original size:21 final size:22
Alignment explanation
Indices: 17476493--17476535 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17476483 AAATAATTTT
*
17476493 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
17476514 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
17476536 TTATTTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:17477345 original size:7 final size:7
Alignment explanation
Indices: 17477335--17477360 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17477325 AAAATAAATC
17477335 GAAAGGA
1 GAAAGGA
17477342 GAAAGGA
1 GAAAGGA
17477349 GAAAGGA
1 GAAAGGA
17477356 GAAAG
1 GAAAG
17477361 AAAGGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
GAAAGGA
Found at i:17477478 original size:15 final size:15
Alignment explanation
Indices: 17477458--17477504 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
17477448 TTATTTTAAA
17477458 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
17477473 TTATATTTAAAATA-
1 TTATATTTTAATTAT
* *
17477487 TTATGTTTTAATCAT
1 TTATATTTTAATTAT
17477502 TTA
1 TTA
17477505 CTTTATTGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:17480379 original size:13 final size:14
Alignment explanation
Indices: 17480355--17480386 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
17480345 CTCACATTTT
17480355 GTTCATAGGTGGAA
1 GTTCATAGGTGGAA
17480369 GTTCA-AGGTGGAA
1 GTTCATAGGTGGAA
17480382 GTTCA
1 GTTCA
17480387 CCACATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.28
Consensus pattern (14 bp):
GTTCATAGGTGGAA
Found at i:17485049 original size:28 final size:28
Alignment explanation
Indices: 17485009--17485155 Score: 91
Period size: 29 Copynumber: 5.1 Consensus size: 28
17484999 AAACGGGACT
*
17485009 TTTTGGATGCTCGGGGGT-AAAATGGTAA
1 TTTTGGATGCTCGAGGGTAAAAATGG-AA
17485037 TTTTGGACT-CTCGAGGGTAAAAATGGAA
1 TTTTGGA-TGCTCGAGGGTAAAAATGGAA
* * * * *
17485065 TTTTTGGAAGTTTGGGGGTAAAAATGTAA
1 -TTTTGGATGCTCGAGGGTAAAAATGGAA
* * ** * *
17485094 TTTTTGGAAGTTTTAGGGTTAAAAATAGAT
1 -TTTTGGATGCTCGAGGG-TAAAAATGGAA
* * * *
17485124 TTTTGGAAGTTTGAGGGTAAAAATGTAA
1 TTTTGGATGCTCGAGGGTAAAAATGGAA
17485152 TTTT
1 TTTT
17485156 TGGAAATTTC
Statistics
Matches: 99, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
28 29 0.29
29 62 0.63
30 8 0.08
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (28 bp):
TTTTGGATGCTCGAGGGTAAAAATGGAA
Found at i:17485060 original size:29 final size:27
Alignment explanation
Indices: 17485009--17485068 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
17484999 AAACGGGACT
*
17485009 TTTTGGATGCTCGGGGGTAAAATGGTAA
1 TTTTGGATGCTCGAGGGTAAAATGG-AA
17485037 TTTTGGACT-CTCGAGGGTAAAAATGGAA
1 TTTTGGA-TGCTCGAGGGT-AAAATGGAA
17485065 TTTT
1 TTTT
17485069 TGGAAGTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (27 bp):
TTTTGGATGCTCGAGGGTAAAATGGAA
Found at i:17485069 original size:29 final size:29
Alignment explanation
Indices: 17485049--17485318 Score: 224
Period size: 29 Copynumber: 9.2 Consensus size: 29
17485039 TTGGACTCTC
17485049 GAGGGTAAAAATGGAATTTTTGGAAGTTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
* *
17485078 GGGGGTAAAAATGTAATTTTTGGAAGTTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
* *
17485107 TAGGGTTAAAAATAG-ATTTTTGGAAGTTT
1 GAGGG-TAAAAATGGAATTTTTGGAAGTTT
* *
17485136 GAGGGTAAAAATGTAATTTTTGGAAATTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
* * * **
17485165 CAGGGTTGAAAATGGAAATTTTACAAGTTT
1 GAGGG-TAAAAATGGAATTTTTGGAAGTTT
*
17485195 G-GGGATAAAAATGTAATTTTTGGAAGTTT
1 GAGGG-TAAAAATGGAATTTTTGGAAGTTT
* * * *
17485224 CAGGATTAAAATGCAATTTTTGGAAGTTT
1 GAGGGTAAAAATGGAATTTTTGGAAGTTT
* * * *
17485253 -AGGGGTCTAAAAATGTAATTTTAGAAAATTT
1 GA-GGG--TAAAAATGGAATTTTTGGAAGTTT
* * **
17485284 CAAGGGTCAAAATATAATTTTTGGATAGTTT
1 -GAGGGTAAAAATGGAATTTTTGGA-AGTTT
17485315 -AGGG
1 GAGGG
17485319 ACCTTTAGGG
Statistics
Matches: 192, Mismatches: 39, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
28 8 0.04
29 115 0.60
30 42 0.22
31 23 0.12
32 3 0.02
33 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
GAGGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:17485101 original size:58 final size:59
Alignment explanation
Indices: 17485021--17485314 Score: 307
Period size: 58 Copynumber: 5.0 Consensus size: 59
17485011 TTGGATGCTC
* *
17485021 GGGGGT-AAAATGGTAA-TTTTGG-ACTCTCGAGGG-TAAAAATGGAATTTTTGGAAGTTT
1 GGGGGTAAAAAT-GTAATTTTTGGAAGTTTC-AGGGTTAAAAATGGAATTTTTGGAAGTTT
* *
17485078 GGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATAG-ATTTTTGGAAGTTT
1 GGGGGTAAAAATGTAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTT
* * * * **
17485136 GAGGGTAAAAATGTAATTTTTGGAAATTTCAGGGTTGAAAATGGAAATTTTACAAGTTT
1 GGGGGTAAAAATGTAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTT
* * *
17485195 GGGGATAAAAATGTAATTTTTGGAAGTTTCAGGATT-AAAATGCAATTTTTGGAAGTTT
1 GGGGGTAAAAATGTAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTT
* * * * *
17485253 AGGGGTCTAAAAATGTAATTTTAGAAAATTTCAAGGGTCAAAATAT--AATTTTTGGATAGTTT
1 -GGGG-GTAAAAATGTAATTTTTGGAAGTTTC-AGGGTTAAAA-ATGGAATTTTTGGA-AGTTT
17485315 AGGGACCTTT
Statistics
Matches: 200, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
57 10 0.05
58 86 0.43
59 58 0.29
60 22 0.11
61 14 0.07
62 8 0.04
63 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (59 bp):
GGGGGTAAAAATGTAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTT
Found at i:17485193 original size:117 final size:118
Alignment explanation
Indices: 17485056--17485290 Score: 325
Period size: 117 Copynumber: 2.0 Consensus size: 118
17485046 CTCGAGGGTA
* ** * * *
17485056 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAAT-
1 AAAATGGAAATTTTACAAGTTTGGGGATAAAAATGTAATTTTTGGAAGTTTCAGGATT-AAAATG
* *
17485120 AGATTTTTGGAAGTTT-GAGGG-TAAAAATGTAATTTTTGGAAATTTC-AGGGTTG
65 A-ATTTTTGGAAGTTTAG-GGGCTAAAAATGTAATTTTAGAAAATTTCAAGGGTTG
17485173 AAAATGGAAATTTTACAAGTTTGGGGATAAAAATGTAATTTTTGGAAGTTTCAGGATTAAAATGC
1 AAAATGGAAATTTTACAAGTTTGGGGATAAAAATGTAATTTTTGGAAGTTTCAGGATTAAAATG-
17485238 AATTTTTGGAAGTTTAGGGGTCTAAAAATGTAATTTTAGAAAATTTCAAGGGT
65 AATTTTTGGAAGTTTAGGGG-CTAAAAATGTAATTTTAGAAAATTTCAAGGGT
17485291 CAAAATATAA
Statistics
Matches: 104, Mismatches: 8, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
116 5 0.05
117 69 0.66
118 2 0.02
119 23 0.22
120 5 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (118 bp):
AAAATGGAAATTTTACAAGTTTGGGGATAAAAATGTAATTTTTGGAAGTTTCAGGATTAAAATGA
ATTTTTGGAAGTTTAGGGGCTAAAAATGTAATTTTAGAAAATTTCAAGGGTTG
Found at i:17487254 original size:6 final size:6
Alignment explanation
Indices: 17487224--17487287 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
17487214 AATATTAAGT
* **
17487224 TTTAAA -TT-AA TTCAAA TTT-AA -TTAAA TTTAAA TTTAAA -GCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
17487267 TTTAAA TTTAAA -ATAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
17487288 GATCAATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
4 4 0.09
5 14 0.32
6 26 0.59
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:17487284 original size:17 final size:17
Alignment explanation
Indices: 17487227--17487287 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
17487217 ATTAAGTTTT
* *
17487227 AAATTAATTCAAATTT-
1 AAATAAATTTAAATTTA
*
17487243 AATTAAATTTAAATTTA
1 AAATAAATTTAAATTTA
**
17487260 AAGCAAATTTAAATTTA
1 AAATAAATTTAAATTTA
17487277 AAATAAATTTA
1 AAATAAATTTA
17487288 GATCAATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
16 13 0.35
17 24 0.65
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATAAATTTAAATTTA
Found at i:17487731 original size:92 final size:92
Alignment explanation
Indices: 17487573--17487984 Score: 734
Period size: 92 Copynumber: 4.5 Consensus size: 92
17487563 TATGTCGAGG
*
17487573 CTTCATCTTGCTCTTACTACAACTTCAAAGAGAGATAAAGACTTGCTATCCAACTTTATTACAAC
1 CTTCATCTTGCTCTTACTACAACTTC--AGAGAGATAAAGACTTGCTATCCAACTTTACTACAAC
* *
17487638 TTCAAGAGGATAGGAATTGATGTTTTAAG
64 TTCAAGAGGATAGGAATTGATGTTTGAAA
17487667 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
17487732 CAAGAGGATAAGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
17487759 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAAACTTGCTATCCAACTTTAGTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
17487824 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
*
17487851 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
17487916 CAAGAGGATAGGGATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
17487943 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTT
17487985 TTCCCTTTTG
Statistics
Matches: 306, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
92 280 0.92
94 26 0.08
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (92 bp):
CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
CAAGAGGATAGGAATTGATGTTTGAAA
Found at i:17487742 original size:40 final size:40
Alignment explanation
Indices: 17487680--17487921 Score: 139
Period size: 40 Copynumber: 5.5 Consensus size: 40
17487670 CATCTTGCTC
*
17487680 TTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACT
1 TTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACT
***
17487720 TTACTACAACTTCA-AGAGGATAAGAATTGATGTTTGAAACTTCATCTTGCT
1 TTACTACAACTTCAGAGA-GAT-A-AA--GA--TTTG---C-T-ATCCAACT
* *
17487771 CTTACTACAACTTCAGAGAGATAAAAACTTGCTATCCAACT
1 -TTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACT
* ***
17487812 TTAGTACAACTTCA-AGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCT
1 TTACTACAACTTCAGAGA-GATA--AA--GA--TTTG---C-T-ATCCAACT
17487863 CTTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACT
1 -TTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACT
17487904 TTACTACAACTTCA-AGAG
1 TTACTACAACTTCAGAGAG
17487922 GATAGGGATT
Statistics
Matches: 155, Mismatches: 19, Indels: 57
0.67 0.08 0.25
Matches are distributed among these distances:
39 10 0.06
40 48 0.31
41 11 0.07
42 6 0.04
43 2 0.01
44 3 0.02
46 13 0.08
48 3 0.02
49 2 0.01
50 6 0.04
51 11 0.07
52 34 0.22
53 6 0.04
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (40 bp):
TTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACT
Found at i:17487877 original size:52 final size:52
Alignment explanation
Indices: 17487816--17487974 Score: 173
Period size: 52 Copynumber: 3.3 Consensus size: 52
17487806 CCAACTTTAG
17487816 TACAACTTCAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTAC
1 TACAACTTCAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTAC
***
17487868 TACAACTTC-AGAGAGATA--AA--GA--TTTG---C-T-ATCCAACT-TTAC
1 TACAACTTCAAGAG-GATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTAC
*
17487908 TACAACTTCAAGAGGATAGGGATTGATGTTTGAAACTTCATCTTGCTCTTAC
1 TACAACTTCAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTAC
17487960 TACAACTTCAGAGAG
1 TACAACTTCA-AGAG
17487975 ATAAAGACTT
Statistics
Matches: 85, Mismatches: 7, Indels: 29
0.70 0.06 0.24
Matches are distributed among these distances:
40 17 0.20
41 9 0.11
42 2 0.02
43 1 0.01
44 2 0.02
46 8 0.09
48 2 0.02
49 1 0.01
50 3 0.04
51 9 0.11
52 27 0.32
53 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (52 bp):
TACAACTTCAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTAC
Found at i:17488091 original size:50 final size:49
Alignment explanation
Indices: 17488037--17488162 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 49
17488027 ACACGGTCTA
* * **
17488037 CCGTTGCGACTTAGACCTTTCCCTT-TTGCCTTTTTGCGGTACTGGATCCG
1 CCGTTGCGACTTAGATCTTTCCCTTCATGCCTTCAT--GGTACTGGATCCG
* * *
17488087 CCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGGTACTGGATTCG
1 CCGTTGC-GACTTAGATCTTTCCCTTCATGCCTTCATGGTACTGGATCCG
* *
17488137 CCGTTGCGGCTTAAATCTTTCCCTTC
1 CCGTTGCGACTTAGATCTTTCCCTTC
17488163 TTATCTTCTG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
49 17 0.26
50 26 0.40
51 16 0.25
52 6 0.09
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (49 bp):
CCGTTGCGACTTAGATCTTTCCCTTCATGCCTTCATGGTACTGGATCCG
Found at i:17488178 original size:50 final size:50
Alignment explanation
Indices: 17488074--17488170 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 50
17488064 GCCTTTTTGC
* *
17488074 GGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCAT
1 GGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATATCTTCAT
* *
17488124 GGTACTGGATTCGCCGTTGCGG-CTTAAATCTTTCCCTTCTTATCTTC
1 GGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATATCTTC
17488171 TGAGGTACGC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 22 0.51
50 21 0.49
ACGTcount: A:0.12, C:0.28, G:0.21, T:0.39
Consensus pattern (50 bp):
GGTACTGGATCCGCCGTTGCGGTCTTAAATCTTTCCCTTCATATCTTCAT
Found at i:17495342 original size:29 final size:29
Alignment explanation
Indices: 17495310--17495403 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
17495300 AAAATGAGAC
*
17495310 TTTTTGGA-TGCTCGAGGG-CAAAATGGTAA
1 TTTTTGGACT-CTCGAGGGAAAAAAT-GTAA
*
17495339 -TTTTAGACTCTCGAGGGAAAAAATGTAA
1 TTTTTGGACTCTCGAGGGAAAAAATGTAA
* *
17495367 TTTTTGGAAGT-TCG-GGGTTAAAAATGTAA
1 TTTTTGG-ACTCTCGAGGG-AAAAAATGTAA
17495396 TTTTTGGA
1 TTTTTGGA
17495404 GTTAAAATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
28 22 0.40
29 31 0.56
30 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTTTGGACTCTCGAGGGAAAAAATGTAA
Found at i:17495441 original size:30 final size:32
Alignment explanation
Indices: 17495407--17495470 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
17495397 TTTTGGAGTT
*
17495407 AAAATGTAATTTT-G-GAAGTTCAGGGGTCAA
1 AAAATGTAATTTTAGAAAAGTTCAGGGGTCAA
17495437 AAAATGTAATTTTAGAAAAGTTCAGGGGTCAA
1 AAAATGTAATTTTAGAAAAGTTCAGGGGTCAA
17495469 AA
1 AA
17495471 TAAAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 13 0.42
31 1 0.03
32 17 0.55
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.28
Consensus pattern (32 bp):
AAAATGTAATTTTAGAAAAGTTCAGGGGTCAA
Found at i:17495471 original size:30 final size:29
Alignment explanation
Indices: 17495407--17495470 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
17495397 TTTTGGAGTT
*
17495407 AAAATGTAATTTTGGAAGTTCAGGGGTCAA
1 AAAATGTAATTTTGAAAGTTCAGGGGTC-A
17495437 AAAATGTAATTTTAGAAAAGTTCAGGGGTCA
1 AAAATGTAATTTT-G-AAAGTTCAGGGGTCA
17495468 AAA
1 AAA
17495471 TAAAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 13 0.42
31 5 0.16
32 13 0.42
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.28
Consensus pattern (29 bp):
AAAATGTAATTTTGAAAGTTCAGGGGTCA
Found at i:17497432 original size:6 final size:6
Alignment explanation
Indices: 17497402--17497504 Score: 67
Period size: 6 Copynumber: 18.0 Consensus size: 6
17497392 AATATTAAGT
* **
17497402 TTTAAA -TT-AA TTCAAA TTT-AA -TTAAA TTTAAA TTTAAA -GCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** ** *
17497445 TTTAAA TTTAAAAA GATAAA TTTAAA TTTAAA TTTAAA GATAAA TTTAGA
1 TTTAAA TTT--AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
17497495 -TT-AA TTTAAA
1 TTTAAA TTTAAA
17497505 CCTAATTTTA
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
4 5 0.07
5 14 0.19
6 49 0.68
8 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:17497450 original size:43 final size:45
Alignment explanation
Indices: 17497402--17497500 Score: 109
Period size: 43 Copynumber: 2.3 Consensus size: 45
17497392 AATATTAAGT
* *
17497402 TTTAAATTAATTCAAA-TTTAA-TTAAATTTAAATTTAAAG-CAAA
1 TTTAAATTAATT-AAAGATAAATTTAAATTTAAATTTAAAGACAAA
*
17497445 TTTAAATTTAA--AAAGATAAATTTAAATTTAAATTTAAAGATAAA
1 TTTAAA-TTAATTAAAGATAAATTTAAATTTAAATTTAAAGACAAA
*
17497489 TTTAGATTAATT
1 TTTAAATTAATT
17497501 TAAACCTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
41 3 0.07
42 3 0.07
43 28 0.61
44 12 0.26
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (45 bp):
TTTAAATTAATTAAAGATAAATTTAAATTTAAATTTAAAGACAAA
Found at i:17497467 original size:20 final size:19
Alignment explanation
Indices: 17497424--17497476 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
17497414 CAAATTTAAT
17497424 TAAATTTAAATTT--AAAG
1 TAAATTTAAATTTAAAAAG
*
17497441 CAAATTTAAATTTAAAAAG
1 TAAATTTAAATTTAAAAAG
17497460 ATAAATTTAAATTTAAA
1 -TAAATTTAAATTTAAA
17497477 TTTAAAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 12 0.39
19 4 0.13
20 15 0.48
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TAAATTTAAATTTAAAAAG
Found at i:17497478 original size:26 final size:26
Alignment explanation
Indices: 17497442--17497504 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 26
17497432 AATTTAAAGC
17497442 AAATTTAAATTTAAAAAGATAAATTT
1 AAATTTAAATTTAAAAAGATAAATTT
17497468 AAATTTAAATTT--AAAGATAAATTT
1 AAATTTAAATTTAAAAAGATAAATTT
*
17497492 AGA-TT-AATTTAAA
1 AAATTTAAATTTAAA
17497505 CCTAATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 5 0.15
23 2 0.06
24 15 0.44
26 12 0.35
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (26 bp):
AAATTTAAATTTAAAAAGATAAATTT
Found at i:17498268 original size:128 final size:127
Alignment explanation
Indices: 17498037--17498285 Score: 349
Period size: 128 Copynumber: 2.0 Consensus size: 127
17498027 TATTATAAAA
*
17498037 AAAATTTAATTTTAATAATTTTGAGACATTAAGTCTCTATATTTTTTATTTAAAAATCTTGATCC
1 AAAATTTAATCTTAATAATTTTGAGACATTAAGTCTCTATATTTTTTATTTAAAAATCTTGATCC
* * * *
17498102 CTCCATCTAATCTTGCCATTAAAGTTTATGGTATCAAAGCTAAATAATTTTTTTTGAAATTT
66 CTCCATCTAATCTTGCCATTAAAATTAATCGTAACAAAGCTAAATAATTTTTTTTGAAATTT
* *
17498164 AAAATTTAATCCTT-ATAATTTTGAGACATTGAGTCT-TGTACTTTTTTTATTTAAAAATCTTGA
1 AAAATTTAAT-CTTAATAATTTTGAGACATTAAGTCTCTATA--TTTTTTATTTAAAAATCTTGA
* * * * *
17498227 TCCTTCCATCTAATTTTTCTATTAAAATTAATCGTAACAAAGGTAAATAATTTTTTTTG
63 TCCCTCCATCTAATCTTGCCATTAAAATTAATCGTAACAAAGCTAAATAATTTTTTTTG
17498286 CATTCAATAT
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
126 3 0.03
127 31 0.29
128 73 0.68
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (127 bp):
AAAATTTAATCTTAATAATTTTGAGACATTAAGTCTCTATATTTTTTATTTAAAAATCTTGATCC
CTCCATCTAATCTTGCCATTAAAATTAATCGTAACAAAGCTAAATAATTTTTTTTGAAATTT
Found at i:17502176 original size:19 final size:19
Alignment explanation
Indices: 17502134--17502178 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
17502124 TTTTATTTTT
*
17502134 ATTAA-TTTAAAATTTTAA
1 ATTAATTTTAAAAATTTAA
*
17502152 A-AAATTTTAAAAATTTAA
1 ATTAATTTTAAAAATTTAA
17502170 ATTAATTTT
1 ATTAATTTT
17502179 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATTTTAAAAATTTAA
Found at i:17502552 original size:36 final size:36
Alignment explanation
Indices: 17502511--17502583 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
17502501 AAGAAAAAGT
17502511 AAAGCTTAAAAATATTAAAGAAAAGATTGTGCTTAG
1 AAAGCTTAAAAATATTAAAGAAAAGATTGTGCTTAG
17502547 AAAGCTTAAAAATATTAAAGAAAAGATTGTGCTTAG
1 AAAGCTTAAAAATATTAAAGAAAAGATTGTGCTTAG
17502583 A
1 A
17502584 CTACACTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (36 bp):
AAAGCTTAAAAATATTAAAGAAAAGATTGTGCTTAG
Found at i:17514216 original size:217 final size:217
Alignment explanation
Indices: 17513841--17514276 Score: 872
Period size: 217 Copynumber: 2.0 Consensus size: 217
17513831 TGATTACATC
17513841 TACTTAGCATGTCGGTGCCCATGCAATAAACTGTTTCCCCATAACACTGAAGATGAGACTTTGGA
1 TACTTAGCATGTCGGTGCCCATGCAATAAACTGTTTCCCCATAACACTGAAGATGAGACTTTGGA
17513906 AGGTTGAATAGAGCTGGCAGCTGTACAAACAATAACACCCACATTGACATGCCCATTAGTTTCTA
66 AGGTTGAATAGAGCTGGCAGCTGTACAAACAATAACACCCACATTGACATGCCCATTAGTTTCTA
17513971 TGCCCACTTTCACTAGGAATAATGTCATCAAGAGTGGTGAAATCAAAAATTTTTTTAGTTACGGT
131 TGCCCACTTTCACTAGGAATAATGTCATCAAGAGTGGTGAAATCAAAAATTTTTTTAGTTACGGT
17514036 GGAAATTAAATTGTATAATTTT
196 GGAAATTAAATTGTATAATTTT
17514058 TACTTAGCATGTCGGTGCCCATGCAATAAACTGTTTCCCCATAACACTGAAGATGAGACTTTGGA
1 TACTTAGCATGTCGGTGCCCATGCAATAAACTGTTTCCCCATAACACTGAAGATGAGACTTTGGA
17514123 AGGTTGAATAGAGCTGGCAGCTGTACAAACAATAACACCCACATTGACATGCCCATTAGTTTCTA
66 AGGTTGAATAGAGCTGGCAGCTGTACAAACAATAACACCCACATTGACATGCCCATTAGTTTCTA
17514188 TGCCCACTTTCACTAGGAATAATGTCATCAAGAGTGGTGAAATCAAAAATTTTTTTAGTTACGGT
131 TGCCCACTTTCACTAGGAATAATGTCATCAAGAGTGGTGAAATCAAAAATTTTTTTAGTTACGGT
17514253 GGAAATTAAATTGTATAATTTT
196 GGAAATTAAATTGTATAATTTT
17514275 TA
1 TA
17514277 AAAAATTAAA
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
217 219 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (217 bp):
TACTTAGCATGTCGGTGCCCATGCAATAAACTGTTTCCCCATAACACTGAAGATGAGACTTTGGA
AGGTTGAATAGAGCTGGCAGCTGTACAAACAATAACACCCACATTGACATGCCCATTAGTTTCTA
TGCCCACTTTCACTAGGAATAATGTCATCAAGAGTGGTGAAATCAAAAATTTTTTTAGTTACGGT
GGAAATTAAATTGTATAATTTT
Found at i:17522903 original size:12 final size:12
Alignment explanation
Indices: 17522886--17522921 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
17522876 TACCAGCTTT
*
17522886 AGCCAAAGCCAA
1 AGCCAAATCCAA
17522898 AGCCAAATCCAA
1 AGCCAAATCCAA
*
17522910 ATCCAAATCCAA
1 AGCCAAATCCAA
17522922 TTTGATATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.33, G:0.08, T:0.08
Consensus pattern (12 bp):
AGCCAAATCCAA
Found at i:17525368 original size:10 final size:10
Alignment explanation
Indices: 17525346--17525435 Score: 59
Period size: 10 Copynumber: 9.6 Consensus size: 10
17525336 TGAAAATCAA
*
17525346 TAAAAACTA-
1 TAAAAATTAT
17525355 TAAAAATTAT
1 TAAAAATTAT
** *
17525365 TAAATTTTAA
1 TAAAAATTAT
17525375 TAAAAA-TA-
1 TAAAAATTAT
17525383 TAAAAA--AT
1 TAAAAATTAT
*
17525391 TAAAAATCAT
1 TAAAAATTAT
*
17525401 T-AAAATGTAG
1 TAAAAAT-TAT
*
17525411 AAAAAATTAT
1 TAAAAATTAT
17525421 TAAAAATTA-
1 TAAAAATTAT
17525430 TAAAAA
1 TAAAAA
17525436 AATTGTAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
7 1 0.02
8 12 0.19
9 21 0.33
10 25 0.39
11 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:17525386 original size:37 final size:38
Alignment explanation
Indices: 17525345--17525435 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 38
17525335 ATGAAAATCA
* * * *
17525345 ATAAAAACTATAAAAATTATTAAATTTTA-ATAAAAA-T
1 ATAAAAAATATAAAAATCATTAAAATGTAGA-AAAAATT
17525382 ATAAAAAAT-TAAAAATCATTAAAATGTAGAAAAAATT
1 ATAAAAAATATAAAAATCATTAAAATGTAGAAAAAATT
*
17525419 ATTAAAAATTATAAAAA
1 A-TAAAAAATATAAAAA
17525436 AATTGTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 21 0.47
37 11 0.24
38 7 0.16
39 6 0.13
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (38 bp):
ATAAAAAATATAAAAATCATTAAAATGTAGAAAAAATT
Found at i:17525403 original size:29 final size:29
Alignment explanation
Indices: 17525344--17525403 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
17525334 GATGAAAATC
* *
17525344 AATAAAAACTATAAAAATTATTAAATTTT
1 AATAAAAACTATAAAAATTATAAAATATT
17525373 AATAAAAA-TATAAAAAATTA-AAAATCATT
1 AATAAAAACTAT-AAAAATTATAAAAT-ATT
17525402 AA
1 AA
17525404 AATGTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (29 bp):
AATAAAAACTATAAAAATTATAAAATATT
Found at i:17525437 original size:21 final size:21
Alignment explanation
Indices: 17525411--17525456 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17525401 TAAAATGTAG
*
17525411 AAAAAATTATTAAAAAT-TATA
1 AAAAAATT-GTAAAAATCTATA
*
17525432 AAAAAATTGTAAAATTCTATA
1 AAAAAATTGTAAAAATCTATA
17525453 AAAA
1 AAAA
17525457 TCGTAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAATTGTAAAAATCTATA
Found at i:17525445 original size:19 final size:19
Alignment explanation
Indices: 17525423--17525473 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
17525413 AAAATTATTA
*
17525423 AAAATTATAAAAAAATTGT
1 AAAATTATAAAAAAATCGT
* *
17525442 AAAATTCTATAAAAATCGT
1 AAAATTATAAAAAAATCGT
17525461 AAAAGTTATAAAA
1 AAAA-TTATAAAA
17525474 TGCATAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (19 bp):
AAAATTATAAAAAAATCGT
Found at i:17525676 original size:19 final size:20
Alignment explanation
Indices: 17525640--17525700 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 20
17525630 TTAGTACAAT
17525640 AATTATTATAATTTTTTACG
1 AATTATTATAATTTTTTACG
17525660 AATT-TTAT-ATTTATTTAC-
1 AATTATTATAATTT-TTTACG
* *
17525678 ATTTTTTTATAATTTTCTTACG
1 A-ATTATTATAATTTT-TTACG
17525700 A
1 A
17525701 CTCTATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 5 0.15
19 11 0.32
20 9 0.26
21 8 0.24
22 1 0.03
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (20 bp):
AATTATTATAATTTTTTACG
Found at i:17525763 original size:29 final size:28
Alignment explanation
Indices: 17525682--17525783 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 28
17525672 ATTTACATTT
* *
17525682 TTTTATAATTTTCTTACGA-CTCTATAAAA
1 TTTTATAATTTTTTTACGATTTCTAT--AA
**
17525711 TTTTATAATTTTTTTCTAATATTTCTATACA
1 TTTTATAA-TTTTTT-TACGATTTCTATA-A
*
17525742 TTTTATAATTTTTTTACGATTTTTATAA
1 TTTTATAATTTTTTTACGATTTCTATAA
17525770 TTTTTAATAATTTT
1 -TTTT-ATAATTTT
17525784 CTTTTTTATT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.02
29 22 0.37
30 20 0.33
31 12 0.20
32 5 0.08
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTATAATTTTTTTACGATTTCTATAA
Found at i:17526091 original size:95 final size:87
Alignment explanation
Indices: 17525899--17526105 Score: 222
Period size: 95 Copynumber: 2.3 Consensus size: 87
17525889 TTAGGGGCGG
*
17525899 TTTAAGTATCCAATTGAGTGAAAAAAAACAAGGCCTTAATGACTTTTTCTGAAAAAGTTTGAAGG
1 TTTAAGTACCCAATTGAGTGAAAAAAAACAAGGCCTTAATGACTTTTTCTGAAAAAGTTTGAAGG
*
17525964 TCTTTTTGATGCATTTTGAAAG
66 TCTTTTTGATGCATTTTGAAAA
* * * *
17525986 TTCAAATACCCAATTGAGTGCAAAATAAAAGCAAGGGCTTAATTG-CTTTTTCTTTTGAAAAATT
1 TTTAAGTACCCAATTGAGTG-AAAA-AAAA-CAAGGCCTTAA-TGACTTTTTC---TGAAAAAGT
* * *
17526050 TTGATAGCTTTTTTTTTATGCATTTTGAAAA
59 TTGA-AG-GTCTTTTTGATGCATTTTGAAAA
*
17526081 TTTAAGTACCCAAATGA--GAAAAAAA
1 TTTAAGTACCCAATTGAGTGAAAAAAA
17526106 TAAAACAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
87 17 0.17
88 4 0.04
89 4 0.04
90 17 0.17
91 5 0.05
92 4 0.04
93 13 0.13
94 2 0.02
95 33 0.33
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (87 bp):
TTTAAGTACCCAATTGAGTGAAAAAAAACAAGGCCTTAATGACTTTTTCTGAAAAAGTTTGAAGG
TCTTTTTGATGCATTTTGAAAA
Found at i:17526329 original size:2 final size:2
Alignment explanation
Indices: 17526318--17526366 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
17526308 AAATACGCTA
17526318 AT AT -T 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 AT AT AT
*
17526359 AT AA AT AT
1 AT AT AT AT
17526367 TTAAGGTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17529045 original size:13 final size:13
Alignment explanation
Indices: 17529029--17529053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17529019 AAAACACTAA
17529029 ATTAAAAAAATAT
1 ATTAAAAAAATAT
17529042 ATTAAAAAAATA
1 ATTAAAAAAATA
17529054 AATAACAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATTAAAAAAATAT
Found at i:17530499 original size:14 final size:15
Alignment explanation
Indices: 17530482--17530515 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17530472 CCACATTCAT
17530482 TTTTCATTAAAA-TG
1 TTTTCATTAAAATTG
*
17530496 TTTTAATTAAAATTG
1 TTTTCATTAAAATTG
17530511 TTTTC
1 TTTTC
17530516 TAATTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTTCATTAAAATTG
Found at i:17531536 original size:27 final size:27
Alignment explanation
Indices: 17531506--17531560 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
17531496 TTTTCGTTTA
*
17531506 ATTTAGAGTTAAATTGATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
* *
17531533 ATTTAAATTTAAATTTATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
17531560 A
1 A
17531561 AATTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (27 bp):
ATTTAAAGTTAAATTGATTTTAAATTT
Found at i:17531542 original size:6 final size:6
Alignment explanation
Indices: 17531524--17531623 Score: 82
Period size: 6 Copynumber: 16.8 Consensus size: 6
17531514 TTAAATTGAT
*
17531524 TTTAAA TTT--A TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A
* * ** * *
17531571 TTTAAA TTT-AC TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TACTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
17531619 TTTAA
1 TTTAA
17531624 CATTAAAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 54 0.71
7 4 0.05
8 6 0.08
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:17531542 original size:17 final size:17
Alignment explanation
Indices: 17531524--17531597 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
17531514 TTAAATTGAT
17531524 TTTAAATTTA-TTTAAA
1 TTTAAATTTACTTTAAA
*
17531540 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
*
17531557 TTTAAATTTA-ATT--A
1 TTTAAATTTACTTTAAA
*
17531571 TTTAAATTTACTTTGAA
1 TTTAAATTTACTTTAAA
17531588 TTTAAATTTA
1 TTTAAATTTA
17531598 AATAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 12 0.23
17 27 0.52
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:17531554 original size:11 final size:10
Alignment explanation
Indices: 17531514--17531591 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 10
17531504 TAATTTAGAG
*
17531514 TTAAATTGATT
1 TTAAATTTA-T
17531525 TTAAATTTAT
1 TTAAATTTAT
17531535 TT-AA---AT
1 TTAAATTTAT
17531541 TTAAATTTATT
1 TTAAATTTA-T
17531552 TTAAATTTAAAT
1 TTAAATTT--AT
17531564 TT-AA-TTAT
1 TTAAATTTAT
17531572 TTAAATTTACT
1 TTAAATTTA-T
*
17531583 TTGAATTTA
1 TTAAATTTA
17531592 AATTTAAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 4 0.07
9 4 0.07
10 9 0.16
11 28 0.51
12 3 0.05
13 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:17532398 original size:3 final size:3
Alignment explanation
Indices: 17532390--17532437 Score: 78
Period size: 3 Copynumber: 15.3 Consensus size: 3
17532380 TTAATATTTG
17532390 ATA ATA ATA ACTA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17532437 A
1 A
17532438 ATAAAAAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:17533438 original size:162 final size:166
Alignment explanation
Indices: 17533256--17533604 Score: 526
Period size: 162 Copynumber: 2.1 Consensus size: 166
17533246 AGCTTTCAAT
*
17533256 TTAGTCCCTTGACTGTTTGACTGTACCAGAGGCTGCCATGTGTCACTTTTTGGCTTATTTATGCA
1 TTAGTCCCTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
17533321 TTTAGTCCTTTTCATTTTTAATTTGTTTTAA-TTT-A-AA-CCCCAAATCAACTTTATTTTAATT
66 TTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTTAATAATCCCCAAATCAACTTTATTTTAATT
* *
17533382 ACAAAATTGGCCCAAGAATTTTTCAAGGTTTATAAA
131 ACAAAATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
17533418 TTAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
1 TTAGTCCCTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
* *
17533483 TTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTGTTTTAATTTAATCCCCAAATTAATTTTATT
66 TTTAGTCCTTTTCATTTTTAATTTGTTTTAA----TTTTAA--TAATCCCCAAATCAACTTTATT
* * *
17533548 TTAATTACGAACTTGGCCCAAGAATTTTTCAAGATTTACAAT
125 TTAATTACAAAATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
17533590 TTAATCCCTTGACTG
1 TTAGTCCCTTGACTG
17533605 CTGAATGCCT
Statistics
Matches: 166, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
162 94 0.57
167 3 0.02
168 1 0.01
171 2 0.01
172 66 0.40
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (166 bp):
TTAGTCCCTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
TTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTTAATAATCCCCAAATCAACTTTATTTTAATT
ACAAAATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:17533513 original size:10 final size:10
Alignment explanation
Indices: 17533498--17533526 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
17533488 TCCTTTTCAT
17533498 TTTTAATTTG
1 TTTTAATTTG
17533508 TTTTAATTTG
1 TTTTAATTTG
17533518 TTTTAATTT
1 TTTTAATTT
17533527 AATCCCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (10 bp):
TTTTAATTTG
Found at i:17533719 original size:29 final size:30
Alignment explanation
Indices: 17533677--17534038 Score: 237
Period size: 29 Copynumber: 12.5 Consensus size: 30
17533667 AAATAGTCTA
*
17533677 AAAATTACCA-TTTT-ACCCTCGAACTTTCT
1 AAAATTACCATTTTTAACCC-CGAACTTTCC
17533706 AAAATT-CCATTTTTAACCCCG-A-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
*
17533735 AAAAATTACCA-TTTTACCCCCGAACTTT-C
1 -AAAATTACCATTTTTAACCCCGAACTTTCC
*
17533764 AAAATT-CTATTTTTAACCCCG-A-TTTCAC
1 AAAATTACCATTTTTAACCCCGAACTTTC-C
*
17533792 TAAAATTACCA-TTTT--CCCTCGAACTTT-T
1 -AAAATTACCATTTTTAACCC-CGAACTTTCC
*
17533820 GAAATT-CCATTTTTAACCCC-AA-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
* *
17533849 AAAATTACCA-TTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTTAACCCCGAACTTTCC
*
17533878 AAAATT-TCATTTTTAACCCCG-A-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
17533907 AAAAATTACC-TTTTT-ACCCTCGAACTTTCC
1 -AAAATTACCATTTTTAACCC-CGAACTTTCC
*
17533937 AAAATT-TCATTTTTAACCCCG-A-TTTCAC
1 AAAATTACCATTTTTAACCCCGAACTTTC-C
*
17533965 TAAAAATTACCA-TTTT-ACCCTTGAACTTTCC
1 --AAAATTACCATTTTTAACCC-CGAACTTTCC
*
17533996 AAAATT-CCATTTTTAACCCTG-A-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
17534025 AAAATTACCATTTT
1 AAAATTACCATTTT
17534039 GCCCCCGGGT
Statistics
Matches: 269, Mismatches: 17, Indels: 93
0.71 0.04 0.25
Matches are distributed among these distances:
26 9 0.03
27 30 0.11
28 34 0.13
29 102 0.38
30 71 0.26
31 13 0.05
32 10 0.04
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCCCGAACTTTCC
Found at i:17533941 original size:59 final size:59
Alignment explanation
Indices: 17533676--17534038 Score: 549
Period size: 59 Copynumber: 6.3 Consensus size: 59
17533666 CAAATAGTCT
*
17533676 AAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
17533735 AAAAATTACCATTTTACCCCCGAACTTT-CAAAATTCTATTTTTAACCCCGATTTCA-C
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* ** *
17533792 TAAAATTACCATTTT-CCCTCGAACTTT-TGAAATTCCATTTTTAACCCCAATTTCACC
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
17533849 -AAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
17533907 AAAAATTACCTTTTTACCCTCGAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACT
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
17533966 AAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACC
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
17534025 -AAAATTACCATTTT
1 AAAAATTACCATTTT
17534039 GCCCCCGGGT
Statistics
Matches: 276, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
56 49 0.18
57 26 0.09
58 66 0.24
59 135 0.49
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:17546264 original size:31 final size:31
Alignment explanation
Indices: 17546222--17546755 Score: 235
Period size: 37 Copynumber: 15.7 Consensus size: 31
17546212 TAACACGTCT
*
17546222 TCAT-CTC-TGAAATTGAAGTAAGAGCAATG
1 TCATCCTCTTGAAATTGAAGTAAGAGCAACG
* **
17546251 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A---GAGCA-ACG
* **
17546287 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
* **
17546319 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A---GAGCA-ACG
* **
17546355 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
* *
17546387 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACAAG
1 TCATCCTCTTGAAATTGAAGTA-AG-AG-CAAC--G
* **
17546423 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
* * *
17546455 TCATCCTTTTGAAATTGAAGTAGAGTGGATAACATG
1 TCATCCTCTTGAAATTGAAGTA-AG-AG-CAAC--G
* ** *
17546491 TCTTTATCTCTGAAATTGAAGTAAGAGTAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
**
17546523 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A---GAGCA-ACG
* **
17546559 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
* *
17546591 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAG
1 TCATCCTCTTGAAATTGAAGTA-AG--AG-CAAC--G
* * *
17546628 TCTTCATCTCTGAAATTGAAGTAAGAGTAACATCAACT
1 TCATCCTCT-TGAAATTGAAGTAAGAG------CAACG
* * *
17546666 TCATCCACTTGAAATTGAAGTAGAGTGGATAACATG
1 TCATCCTCTTGAAATTGAAGTA-AG-AG-CAAC--G
* **
17546702 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
*
17546734 TCATCCTCTTGAAATTAAAGTA
1 TCATCCTCTTGAAATTGAAGTA
17546756 GAGTTGGATA
Statistics
Matches: 375, Mismatches: 81, Indels: 96
0.68 0.15 0.17
Matches are distributed among these distances:
29 4 0.01
30 2 0.01
31 90 0.24
32 55 0.15
33 11 0.03
34 20 0.05
35 16 0.04
36 51 0.14
37 101 0.27
38 21 0.06
39 1 0.00
40 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (31 bp):
TCATCCTCTTGAAATTGAAGTAAGAGCAACG
Found at i:17546299 original size:68 final size:68
Alignment explanation
Indices: 17546185--17547164 Score: 1352
Period size: 68 Copynumber: 13.9 Consensus size: 68
17546175 ATCATTTCCA
* * * *
17546185 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
17546250 GTC
66 GTC
* *
17546253 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
17546318 GTC
66 GTC
* *
17546321 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
17546386 GTC
66 GTC
17546389 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
17546454 GTC
66 GTC
* * *
17546457 ATCCTTTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGTAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
17546522 GTC
66 GTC
*
17546525 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
17546590 GTC
66 GTC
*
17546593 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG---
*
17546658 CATCAACTTC
62 ---CAACGTC
* *
17546668 ATCCACTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
17546733 GTC
66 GTC
* *
17546736 ATCCTCTTGAAATTAAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAGGAGCAG
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA-
*
17546801 GATCATTTCC
64 -A-C--GT-C
* * *
17546811 TATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTA
1 -ATCCTCTTGAAATTGAAGT-AGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG--
*
17546876 ACATCGTTTCC
62 -CAACG--T-C
* * * *
17546887 TATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGAAAGAGCA
1 -ATCCTCTTGAAATTGAAGT-AGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
17546952 ACGTC
64 ACGTC
* *
17546957 ATCCTCTAGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAG---
*
17547022 CATCAACTTC
62 ---CAACGTC
*
17547032 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACA-TCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACA-AGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
17547096 CGTC
65 CGTC
*
17547100 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACA-CCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACA-AGTCTTTATCTCTGAAATTGAAGTAAGAGCA
17547164 A
64 A
17547165 GATCATTTCC
Statistics
Matches: 837, Mismatches: 45, Indels: 59
0.89 0.05 0.06
Matches are distributed among these distances:
68 409 0.49
69 167 0.20
70 1 0.00
71 2 0.00
72 1 0.00
73 4 0.00
74 72 0.09
75 57 0.07
76 120 0.14
77 2 0.00
79 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (68 bp):
ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:17547526 original size:27 final size:27
Alignment explanation
Indices: 17547496--17547554 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
17547486 GGACTTTTCG
**
17547496 TTTAATTGGAGTTAAATTGATTTTAAA
1 TTTAATTAAAGTTAAATTGATTTTAAA
* * *
17547523 TTTATTTAAATTTAAATTTATTTTAAA
1 TTTAATTAAAGTTAAATTGATTTTAAA
17547550 TTTAA
1 TTTAA
17547555 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (27 bp):
TTTAATTAAAGTTAAATTGATTTTAAA
Found at i:17547535 original size:6 final size:6
Alignment explanation
Indices: 17547517--17547647 Score: 101
Period size: 6 Copynumber: 21.8 Consensus size: 6
17547507 TTAAATTGAT
*
17547517 TTTAAA TTT--A TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A
* * * *
17547564 TTTAAA TTT-AC TTTGAA TTTAAA TTTAATTA TTTAAA TTT-AC TTTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA
** * *
17547612 TTTAAA TTTAAA TAAAAA TTAAAA TACTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA
17547648 CATTAAAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.04
5 12 0.12
6 69 0.68
7 4 0.04
8 12 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:17547547 original size:11 final size:10
Alignment explanation
Indices: 17547507--17547615 Score: 63
Period size: 11 Copynumber: 10.9 Consensus size: 10
17547497 TTAATTGGAG
*
17547507 TTAAATTGATT
1 TTAAATTTA-T
17547518 TTAAATTTAT
1 TTAAATTTAT
17547528 TT-AA---AT
1 TTAAATTTAT
17547534 TTAAATTTATT
1 TTAAATTTA-T
17547545 TTAAATTTAAAT
1 TTAAATTT--AT
17547557 TT-AA-TTAT
1 TTAAATTTAT
17547565 TTAAATTTACT
1 TTAAATTTA-T
*
17547576 TTGAATTTAAAT
1 TTAAATTT--AT
17547588 TT-AA-TTAT
1 TTAAATTTAT
17547596 TTAAATTTACT
1 TTAAATTTA-T
*
17547607 TTGAATTTA
1 TTAAATTTA
17547616 AATTTAAATA
Statistics
Matches: 80, Mismatches: 3, Indels: 30
0.71 0.03 0.27
Matches are distributed among these distances:
6 4 0.05
7 2 0.03
8 8 0.10
9 6 0.08
10 14 0.17
11 38 0.47
12 6 0.08
13 2 0.03
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:17547547 original size:17 final size:15
Alignment explanation
Indices: 17547517--17547621 Score: 115
Period size: 17 Copynumber: 6.7 Consensus size: 15
17547507 TTAAATTGAT
17547517 TTTAAATTTATTTAAA
1 TTTAAATTTATTT-AA
17547533 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTT-AA
*
17547550 TTTAAATTTAATT-A
1 TTTAAATTTATTTAA
17547564 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTT-AA
*
17547581 TTTAAATTTAATT-A
1 TTTAAATTTATTTAA
17547595 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTT-AA
17547612 TTTAAATTTA
1 TTTAAATTTA
17547622 AATAAAAATT
Statistics
Matches: 78, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
14 22 0.28
15 4 0.05
16 14 0.18
17 38 0.49
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTAAATTTATTTAA
Found at i:17547570 original size:31 final size:31
Alignment explanation
Indices: 17547507--17547622 Score: 159
Period size: 31 Copynumber: 3.9 Consensus size: 31
17547497 TTAATTGGAG
* *
17547507 TTAAATTGATTTTAAATTT--ATTTAA--AT
1 TTAAATTTACTTTAAATTTAAATTTAATTAT
*
17547534 TTAAATTTATTTTAAATTTAAATTTAATTAT
1 TTAAATTTACTTTAAATTTAAATTTAATTAT
*
17547565 TTAAATTTACTTTGAATTTAAATTTAATTAT
1 TTAAATTTACTTTAAATTTAAATTTAATTAT
*
17547596 TTAAATTTACTTTGAATTTAAATTTAA
1 TTAAATTTACTTTAAATTTAAATTTAA
17547623 ATAAAAATTA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
27 18 0.22
29 6 0.07
31 58 0.71
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (31 bp):
TTAAATTTACTTTAAATTTAAATTTAATTAT
Found at i:17548422 original size:3 final size:3
Alignment explanation
Indices: 17548414--17548468 Score: 74
Period size: 3 Copynumber: 17.3 Consensus size: 3
17548404 TTAATATTTG
*
17548414 ATA ATA ATA ACTA ATA ATAA ATA TTA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA A-TA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A
17548462 ATA ATA A
1 ATA ATA A
17548469 AAAGGAATTG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 38 0.81
4 9 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17548428 original size:10 final size:9
Alignment explanation
Indices: 17548414--17548468 Score: 74
Period size: 10 Copynumber: 5.8 Consensus size: 9
17548404 TTAATATTTG
17548414 ATAATAATA
1 ATAATAATA
17548423 ACTAATAATAA
1 A-TAATAAT-A
*
17548434 ATATTAATA
1 ATAATAATA
17548443 ATAATAATA
1 ATAATAATA
17548452 ATAATAATAA
1 ATAATAAT-A
17548462 ATAATAA
1 ATAATAA
17548469 AAAGGAATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 18 0.44
10 21 0.51
11 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAATAATA
Found at i:17548430 original size:13 final size:12
Alignment explanation
Indices: 17548414--17548468 Score: 74
Period size: 13 Copynumber: 4.3 Consensus size: 12
17548404 TTAATATTTG
17548414 ATAATAATAACTA
1 ATAATAATAA-TA
*
17548427 ATAATAAATATTA
1 ATAAT-AATAATA
17548440 ATAATAATAATA
1 ATAATAATAATA
17548452 ATAATAATAAATA
1 ATAATAAT-AATA
17548465 ATAA
1 ATAA
17548469 AAAGGAATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
12 14 0.37
13 20 0.53
14 4 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATAATAATA
Found at i:17549569 original size:29 final size:30
Alignment explanation
Indices: 17549527--17549889 Score: 278
Period size: 29 Copynumber: 12.5 Consensus size: 30
17549517 AAACAGTCCA
*
17549527 AAAATTACCA-TTTTATCCCCGAACTTTCC
1 AAAATTACCATTTTTAACCCCGAACTTTCC
17549556 AAAATT-CCATTTTTAACCCCG-A-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
17549585 AAAGATTACCA-TTTT-ACCCTCGAAC-TTCC
1 AAA-ATTACCATTTTTAACCC-CGAACTTTCC
*
17549614 AAAATT-CTATTTTTAACCCCG-A-TTTCAC
1 AAAATTACCATTTTTAACCCCGAACTTTC-C
** *
17549642 TAAAATTACCA-TTTTGCCCCCAAAC-TTCC
1 -AAAATTACCATTTTTAACCCCGAACTTTCC
*
17549671 AAAATT-CCATTTTTAACCTCG-A-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
17549700 AAAATTACCA-TTTT-ACCCTCGAACTTTCC
1 AAAATTACCATTTTTAACCC-CGAACTTTCC
*
17549729 AAAATT-CCATTTTTAACCTCG-A-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
* *
17549758 AAAAATTACC-TTTTTACCCCCAAACTTTCC
1 -AAAATTACCATTTTTAACCCCGAACTTTCC
17549788 AAAATT-CCATTTTTAACCCCG-A-TTTCAC
1 AAAATTACCATTTTTAACCCCGAACTTTC-C
*
17549816 TAAAAATTACCA-TTTTACCCCCGAACTTTCC
1 --AAAATTACCATTTTTAACCCCGAACTTTCC
*
17549847 AAAATT-CCATTTTTAACCTCG-A-TTTCACC
1 AAAATTACCATTTTTAACCCCGAACTTT--CC
17549876 AAAATTACCATTTT
1 AAAATTACCATTTT
17549890 GCCCCAGGGT
Statistics
Matches: 271, Mismatches: 20, Indels: 85
0.72 0.05 0.23
Matches are distributed among these distances:
27 25 0.09
28 42 0.15
29 118 0.44
30 62 0.23
31 17 0.06
32 7 0.03
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCCCGAACTTTCC
Found at i:17549792 original size:59 final size:59
Alignment explanation
Indices: 17549524--17549894 Score: 572
Period size: 59 Copynumber: 6.4 Consensus size: 59
17549514 CCCAAACAGT
*
17549524 CCAAAAATTACCATTTTATCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
17549583 CCAAAGATTACCATTTTACCCTCGAAC-TTCCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
17549641 -CTAAAATTACCATTTTGCCCCCAAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
17549698 CC-AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
17549756 CCAAAAATTACCTTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
17549815 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
17549874 CC-AAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
17549895 AGGGTATCCA
Statistics
Matches: 285, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
57 71 0.25
58 82 0.29
59 132 0.46
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:17561927 original size:95 final size:95
Alignment explanation
Indices: 17561745--17562449 Score: 930
Period size: 95 Copynumber: 7.4 Consensus size: 95
17561735 AAATAAGCAA
* * *
17561745 GAAGTAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTTAAAATCCCATCTTCT
1 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGAC-TTCAAATCCCATCTTCC
17561810 TGGTGAGGTACAGAGAAGTGGGTCAAAACAG
65 TGGTGAGGTACAGAGAAGTGGGTCAAAACAG
* * * * *
17561841 GAAGCAGAGCTCAATGTCCCTAAGGTTATAGTGGAGTTGAGTGAGACTTCAAATCCCATCTTCCT
1 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCT
* *
17561906 AGTGAGGTACAGAGAAGTGGGTCAAAATAG
66 GGTGAGGTACAGAGAAGTGGGTCAAAACAG
* * *
17561936 GAAGCAGAGCTCAATGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTTAAATCCCATCTTCCT
1 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCT
* * *
17562001 GGTAAGGTAGAGAGAAGTGGGTTAAAACAG
66 GGTGAGGTACAGAGAAGTGGGTCAAAACAG
* * * *
17562031 GAAGCAGAGCTCAACGT-CTATGAGGTTACAATGAAGTGGAGTGAGACTTCAAATCTCATCTTTC
1 GAAGCAGAGCTCAACGTCCT-TGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCC
* * * * *
17562095 TGGTAAGGTATAAAGAAGTAGGTCAAAACAA
65 TGGTGAGGTACAGAGAAGTGGGTCAAAACAG
* * * ** * *
17562126 GAAGCAGAGCTCATCGTCCTTGAGGTTATATTGCTGTGGAGTGTGACTGCAAATCCCATCTTCCT
1 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCT
*
17562191 GGTGAGGTACAGAGAAGTGGGTCAAAATAG
66 GGTGAGGTACAGAGAAGTGGGTCAAAACAG
* * * * *
17562221 GTAGTAGAGCTCAACGTCCTTGAGGTTATAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTTCT
1 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCT
*
17562286 GGTGAGGTATAGAGAAGTGGGTCAAATA-A-
66 GGTGAGGTACAGAGAAGTGGGTCAAA-ACAG
* * *
17562315 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTAAGACTTCAAATCTCATCTTTCT
1 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCT
* *
17562380 AGTGAGGTACAGAGAAGTGGGCCAAAACAG
66 GGTGAGGTACAGAGAAGTGGGTCAAAACAG
* * * *
17562410 GTAGCAGATCTCAACGTCCCTGAGGTTACAGTAGAGTGGA
1 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGA
17562450 ATGAAGCACC
Statistics
Matches: 534, Mismatches: 70, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
93 1 0.00
94 84 0.16
95 405 0.76
96 44 0.08
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (95 bp):
GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCT
GGTGAGGTACAGAGAAGTGGGTCAAAACAG
Found at i:17562510 original size:189 final size:185
Alignment explanation
Indices: 17561645--17562638 Score: 818
Period size: 190 Copynumber: 5.2 Consensus size: 185
17561635 AGCACATTTT
* * *
17561645 ACAGGTAACAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGAAGTGAAGAAC-CAAATCCTATA
1 ACAGGTAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGAA-TG-AG-ACTCAAATCATAT-
* ** * * * *
17561709 CCCT-TGAGTTGCAGTG-GGTCAGATGAAAATAAGCAAGAAGTAGAGCTCAACGTCCTTGAGGTT
62 CCCTGTGAGGTATAGAGAAGT-AGAT--CAA-AA-CAAGAAGCAGAGCTCAACGTCCTTGAGGTT
* *
17561772 ACAGTGGAGTGGAGTGAGACTTTAAAATCCCATCTTCTTGGTGAGGTACAGAGAAGTGGGTCAAA
122 ACAGTGGAGTGGAGTGAGAC-TTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAA
* * * * * *
17561837 ACAGGAAGCAGAGCTCAATGTCCCTAAGGTTATAGTGGAGTTGAGTGAGACTTCAAATCCCATCT
1 ACAGGTAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAG-TGAATGAGAC-TCAAAT--CATAT
* * * * * * * *
17561902 TCCTAGTGAGGTACAGAGAAGTGGGTCAAAATAGGAAGCAGAGCTCAATGTCCCTGAGGTTACAG
62 CCCT-GTGAGGTATAGAGAAGTAGATCAAAACAAGAAGCAGAGCTCAACGTCCTTGAGGTTACAG
* * * *
17561967 TGGAGTGGAGTGAGACTTTAAATCCCATCTTCCTGGTAAGGTAGAGAGAAGTGGGTTAAA
126 TGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAA
* ** * * *
17562027 ACAGGAAGCAGAGCTCAACGTCTATGAGGTTACAATGAAGTGGAGTGAGACTTCAAATC-TCATC
1 ACAGGTAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGT-GAATGAGAC-TCAAATCAT-ATC
* * * * * *
17562091 TTTCTGGTAAGGTATAAAGAAGTAGGTCAAAACAAGAAGCAGAGCTCATCGTCCTTGAGGTTATA
63 --CCT-GTGAGGTATAGAGAAGTAGATCAAAACAAGAAGCAGAGCTCAACGTCCTTGAGGTTACA
* ** * *
17562156 TTGCTGTGGAGTGTGACTGCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAA
125 GTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAA
* * * * * *
17562217 ATAGGTAGTAGAGCTCAACGTCCTTGAGGTTATAGTGGAGTAGAGTGAGACTTCAAATCCCATCT
1 ACAGGTAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGT-GAATGAGAC-TCAAAT--CATAT
** * * *
17562282 TTCTGGTGAGGTATAGAGAAGTGGGTC-AAATAAGAAGCAGAGCTCAACGTCCTTGAGGTTACAG
62 CCCT-GTGAGGTATAGAGAAGTAGATCAAAACAAGAAGCAGAGCTCAACGTCCTTGAGGTTACAG
* * * * *
17562346 TGGAGTGGAGTAAGACTTCAAATCTCATCTTTCTAGTGAGGTACAGAGAAGTGGGCCAAA
126 TGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAA
* *
17562406 ACAGGTAGCAGATCTCAACGTCCCTGAGGTTACAGTAGAGTGGAATGAAGCAC-CAAAATCATAT
1 ACAGGTAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGT-GAATG-AG-ACTC-AAATCATAT
* * * * * * * * * *
17562470 ACCCT-TGAGTTGTAGTG-GGTCAGATTAAAACAATGAAGCAGAGCTCAACATCCCTAAGATTTC
62 -CCCTGTGAGGTATAGAGAAGT-AGATCAAAACAA-GAAGCAGAGCTCAACGTCCTTGAGGTTAC
* * * * * * *
17562533 AATAGAGTAGAGTGAGTCTTTAAATCCCATCTTACTGGTGAAGTACAGAGAAGTGGGAT-AAA
124 AGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGG-TCAAA
* * * * * * *
17562595 ATAGGTAGCAAATCTCATCGTCCTTGAGGTTATAGTGAAGTGAA
1 ACAGGTAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGAA
17562639 GTGAAGCACC
Statistics
Matches: 653, Mismatches: 126, Indels: 50
0.79 0.15 0.06
Matches are distributed among these distances:
186 2 0.00
187 12 0.02
188 14 0.02
189 235 0.36
190 271 0.42
191 49 0.08
192 45 0.07
193 9 0.01
194 3 0.00
195 11 0.02
196 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (185 bp):
ACAGGTAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGAATGAGACTCAAATCATATCCCT
GTGAGGTATAGAGAAGTAGATCAAAACAAGAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAG
TGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGTCAAA
Found at i:17562646 original size:189 final size:189
Alignment explanation
Indices: 17562315--17562697 Score: 473
Period size: 189 Copynumber: 2.0 Consensus size: 189
17562305 GGTCAAATAA
* * * * * * * * *
17562315 GAAGCAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTAAGACTTCAAATCTCATCTTTCT
1 GAAGCAGAGCTCAACATCCCTAAGATTACAATAGAGTAGAGTAAGACTTCAAATCCCATCTTACT
* * *
17562380 AGTGAGGTACAGAGAAGTGGGCCAAAACAGGTAGCAGATCTCAACGTCCCTGAGGTTACAGTAGA
66 AGTGAAGTACAGAGAAGTGGGACAAAACAGGTAGCAAATCTCAACGTCCCTGAGGTTACAGTAGA
* *
17562445 GTGGAATGAAGCACCAAAATCATATACCCTTGAGTTGTAGTGGGTCAGATTAAAACAAT
131 GTGGAATGAAGCACCAAAATCATATACCCTTGAGTTGTAGAGGGTCAGATGAAAACAAT
* * * *
17562504 GAAGCAGAGCTCAACATCCCTAAGATTTCAATAGAGTAGAGTGAGTCTTTAAATCCCATCTTACT
1 GAAGCAGAGCTCAACATCCCTAAGATTACAATAGAGTAGAGTAAGACTTCAAATCCCATCTTACT
* * * * * *
17562569 GGTGAAGTACAGAGAAGTGGGATAAAATAGGTAGCAAATCTCATCGTCCTTGAGGTTATAGT-GA
66 AGTGAAGTACAGAGAAGTGGGACAAAACAGGTAGCAAATCTCAACGTCCCTGAGGTTACAGTAG-
* * * * *
17562633 AGT-GAAGTGAAGCACCAGAATCCTATACCCTTGAGTTGTAGAGGGTCGGATGCAAATAAT
130 AGTGGAA-TGAAGCACCAAAATCATATACCCTTGAGTTGTAGAGGGTCAGATGAAAACAAT
17562693 GAAGC
1 GAAGC
17562698 GAAGCTTCAA
Statistics
Matches: 163, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
188 4 0.02
189 159 0.98
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (189 bp):
GAAGCAGAGCTCAACATCCCTAAGATTACAATAGAGTAGAGTAAGACTTCAAATCCCATCTTACT
AGTGAAGTACAGAGAAGTGGGACAAAACAGGTAGCAAATCTCAACGTCCCTGAGGTTACAGTAGA
GTGGAATGAAGCACCAAAATCATATACCCTTGAGTTGTAGAGGGTCAGATGAAAACAAT
Found at i:17564549 original size:5 final size:5
Alignment explanation
Indices: 17564539--17564583 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
17564529 AATCCTATTT
*
17564539 TTTTA TTTTA TTTTA -TTTA TTTAATA TTTTA TTTTA TGTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTT--TA TTTTA TTTTA TTTTA TTTT
17564584 CAACCTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
5 26 0.74
7 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:17564568 original size:21 final size:22
Alignment explanation
Indices: 17564542--17564582 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
17564532 CCTATTTTTT
17564542 TATTTTATTTTAT-TTATTTAA
1 TATTTTATTTTATGTTATTTAA
17564563 TATTTTATTTTATGTTATTT
1 TATTTTATTTTATGTTATTT
17564583 TCAACCTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTTATTTTATGTTATTTAA
Found at i:17564738 original size:15 final size:14
Alignment explanation
Indices: 17564706--17564732 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17564696 CCGCATTCAT
17564706 TTTTAATTAAAATA
1 TTTTAATTAAAATA
17564720 TTTTAATTAAAAT
1 TTTTAATTAAAAT
17564733 TGTTTTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTAATTAAAATA
Found at i:17565663 original size:6 final size:6
Alignment explanation
Indices: 17565652--17565686 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
17565642 TTTTTTCTGC
*
17565652 TCTCCT TCTCCT TCTCCT TCCCCT TCTCCT TCTCC
1 TCTCCT TCTCCT TCTCCT TCTCCT TCTCCT TCTCC
17565687 AGCCTTACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (6 bp):
TCTCCT
Found at i:17566472 original size:13 final size:13
Alignment explanation
Indices: 17566454--17566488 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
17566444 TAATTTTATA
17566454 TTTAAAAAATATT
1 TTTAAAAAATATT
17566467 TTT--AAAATATT
1 TTTAAAAAATATT
17566478 TTTAAAAAATA
1 TTTAAAAAATA
17566489 ATTAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:17569100 original size:20 final size:20
Alignment explanation
Indices: 17569075--17569130 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
17569065 TGGTGTTTGA
17569075 AGTTTAAGGTTCAAGGTTCG
1 AGTTTAAGGTTCAAGGTTCG
* * *
17569095 AGTTTAAAGTTCGAGGTTCT
1 AGTTTAAGGTTCAAGGTTCG
*
17569115 AGATTTTAGGTTCAAG
1 AG-TTTAAGGTTCAAG
17569131 ATACAAGAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.38
Consensus pattern (20 bp):
AGTTTAAGGTTCAAGGTTCG
Found at i:17572523 original size:28 final size:28
Alignment explanation
Indices: 17572491--17572569 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
17572481 AAGACTCAAG
17572491 ACCTTGGATCCTAAATCCTAGACCTTAA
1 ACCTTGGATCCTAAATCCTAGACCTTAA
* *
17572519 ACCTTGGA-CCTTAAATCTTAGACCTTGA
1 ACCTTGGATCC-TAAATCCTAGACCTTAA
* * *
17572547 ACTTTGAAATCCTAAACCCTAGA
1 ACCTTG-GATCCTAAATCCTAGA
17572570 TGAACCCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 2 0.05
28 28 0.67
29 10 0.24
30 2 0.05
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (28 bp):
ACCTTGGATCCTAAATCCTAGACCTTAA
Found at i:17572528 original size:14 final size:14
Alignment explanation
Indices: 17572509--17572544 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17572499 TCCTAAATCC
17572509 TAGACCTTAAACCT
1 TAGACCTTAAACCT
* *
17572523 TGGACCTTAAATCT
1 TAGACCTTAAACCT
17572537 TAGACCTT
1 TAGACCTT
17572545 GAACTTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (14 bp):
TAGACCTTAAACCT
Found at i:17572581 original size:110 final size:112
Alignment explanation
Indices: 17572416--17572698 Score: 392
Period size: 110 Copynumber: 2.5 Consensus size: 112
17572406 TAAATTTTAA
* *
17572416 ACCCTAAATCTTAGACATTAAACTTTAAAATCCTAAACCCTAGATAAACCCTAAAACATAGACCC
1 ACCCTAAATCTTAGACCTTAAACTTT-AAATCCTAAACCCTAGATGAACCCTAAAACATAGACCC
* * *
17572481 AAGACTCAAGACCTTGGA-T-CC-TAAATCCTAGACCTTAAACCTTGG
65 AAGACTCAAAACCTTAGACTACCTTAAATCCTAAACCTTAAACCTTGG
* * *
17572526 ACCTTAAATCTTAGACCTTGAACTTTGAAATCCTAAACCCTAGATGAACCCTAAAACCTAGACCC
1 ACCCTAAATCTTAGACCTTAAACTTT-AAATCCTAAACCCTAGATGAACCCTAAAACATAGACCC
*
17572591 AAGACTCAAAACCTTAGACCTTAGACCTTAAATCCTAAACCTTAAACGTTGG
65 AAGACTCAAAACCTTAGA-C-T--ACCTTAAATCCTAAACCTTAAACCTTGG
* *
17572643 ACCCTAAATCTTAGACCTTAAACATTAAATCTTAAACCCTAGATGAACCCTAAAAC
1 ACCCTAAATCTTAGACCTTAAACTTTAAATCCTAAACCCTAGATGAACCCTAAAAC
17572699 TTAAACTCGA
Statistics
Matches: 152, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
110 75 0.49
113 1 0.01
116 31 0.20
117 45 0.30
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (112 bp):
ACCCTAAATCTTAGACCTTAAACTTTAAATCCTAAACCCTAGATGAACCCTAAAACATAGACCCA
AGACTCAAAACCTTAGACTACCTTAAATCCTAAACCTTAAACCTTGG
Found at i:17572636 original size:7 final size:7
Alignment explanation
Indices: 17572599--17572804 Score: 92
Period size: 7 Copynumber: 28.7 Consensus size: 7
17572589 CCAAGACTCA
17572599 AAACCTT
1 AAACCTT
*
17572606 AGACCTT
1 AAACCTT
*
17572613 AGACCTT
1 AAACCTT
17572620 AAATCC-T
1 AAA-CCTT
17572627 AAACCTT
1 AAACCTT
*
17572634 AAACGTT
1 AAACCTT
** *
17572641 GGACCCT
1 AAACCTT
*
17572648 AAATCTT
1 AAACCTT
*
17572655 AGACCTT
1 AAACCTT
*
17572662 AAACATT
1 AAACCTT
*
17572669 AAATCTT
1 AAACCTT
17572676 AAACCCTAGAT
1 AAA-CCT---T
* *
17572687 GAACCCT
1 AAACCTT
*
17572694 AAAACTT
1 AAACCTT
*
17572701 AAA-CTCG
1 AAACCT-T
*
17572708 AGACCTT
1 AAACCTT
*
17572715 ACACCTT
1 AAACCTT
* *
17572722 AAATCGT
1 AAACCTT
*
17572729 AGACCTT
1 AAACCTT
17572736 AAACCTT
1 AAACCTT
*
17572743 GAACCTT
1 AAACCTT
*
17572750 GAACCTT
1 AAACCTT
*
17572757 GAACCTT
1 AAACCTT
*
17572764 GAACCTT
1 AAACCTT
*
17572771 AAATCTT
1 AAACCTT
*
17572778 AAACTTT
1 AAACCTT
*
17572785 AAATCTT
1 AAACCTT
*
17572792 AAAATCTT
1 -AAACCTT
17572800 AAACC
1 AAACC
17572805 CTAGATAAAC
Statistics
Matches: 148, Mismatches: 42, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
6 4 0.03
7 126 0.85
8 13 0.09
10 2 0.01
11 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (7 bp):
AAACCTT
Found at i:17572856 original size:14 final size:14
Alignment explanation
Indices: 17572839--17572874 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17572829 CCAAGATTCG
17572839 AGACCTTGAACCTT
1 AGACCTTGAACCTT
* *
17572853 AGACCTTAAACTTT
1 AGACCTTGAACCTT
17572867 AGACCTTG
1 AGACCTTG
17572875 CATCCTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (14 bp):
AGACCTTGAACCTT
Found at i:17573988 original size:28 final size:28
Alignment explanation
Indices: 17573931--17574060 Score: 142
Period size: 28 Copynumber: 4.7 Consensus size: 28
17573921 ATTTAGAGAT
*
17573931 AGCCACAAAGGTGTC-CTTT-ACAGAA-TC
1 AGCCACAAAGG-CTCACTTTAACA-AATTC
*
17573958 AGCCACAAAAGCTCACTTTAACAAATTC
1 AGCCACAAAGGCTCACTTTAACAAATTC
* * *
17573986 AGCCACAAAGGCTTACTTTAATAAATTT
1 AGCCACAAAGGCTCACTTTAACAAATTC
* *
17574014 AGCCACAGAGGCTCACGTTAACAGAA-TC
1 AGCCACAAAGGCTCACTTTAACA-AATTC
17574042 AGCCACAAAGGCTCACTTT
1 AGCCACAAAGGCTCACTTT
17574061 TTAGAAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.02
27 16 0.19
28 66 0.77
29 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (28 bp):
AGCCACAAAGGCTCACTTTAACAAATTC
Found at i:17581976 original size:30 final size:30
Alignment explanation
Indices: 17581940--17582017 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 30
17581930 TAGCTAAGCT
* *
17581940 ACCAAATCCCCCACCACCTGAAGCCAGACC
1 ACCAAATCCCCCACCACCTGAAGCAACACC
17581970 ACCAAAT---CCACCACCTGAAGCAACACC
1 ACCAAATCCCCCACCACCTGAAGCAACACC
* *
17581997 A-GAAAACCCACCACCACCTGA
1 ACCAAATCCC-CCACCACCTGA
17582018 GGCAGGAGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 3 0.08
27 19 0.47
30 18 0.45
ACGTcount: A:0.38, C:0.46, G:0.09, T:0.06
Consensus pattern (30 bp):
ACCAAATCCCCCACCACCTGAAGCAACACC
Found at i:17582122 original size:174 final size:174
Alignment explanation
Indices: 17581832--17582191 Score: 711
Period size: 174 Copynumber: 2.1 Consensus size: 174
17581822 CTCCTGCGAA
17581832 ACCACCACCTGAGGCAGGAGCAGCAAATCCTCCAGTACCACCACCAGCAGCTCCAGCAAATCCAC
1 ACCACCACCTGAGGCAGGAGCAGCAAATCCTCCAGTACCACCACCAGCAGCTCCAGCAAATCCAC
*
17581897 CTCCACCGGAGGCAGAACCTGTAAGTCCTCCACTAGCTAAGCTACCAAATCCCCCACCACCTGAA
66 CACCACCGGAGGCAGAACCTGTAAGTCCTCCACTAGCTAAGCTACCAAATCCCCCACCACCTGAA
17581962 GCCAGACCACCAAATCCACCACCTGAAGCAACACCAGAAAACCC
131 GCCAGACCACCAAATCCACCACCTGAAGCAACACCAGAAAACCC
17582006 ACCACCACCTGAGGCAGGAGCAGCAAATCCTCCAGTACCACCACCAGCAGCTCCAGCAAATCCAC
1 ACCACCACCTGAGGCAGGAGCAGCAAATCCTCCAGTACCACCACCAGCAGCTCCAGCAAATCCAC
17582071 CACCACCGGAGGCAGAACCTGTAAGTCCTCCACTAGCTAAGCTACCAAATCCCCCACCACCTGAA
66 CACCACCGGAGGCAGAACCTGTAAGTCCTCCACTAGCTAAGCTACCAAATCCCCCACCACCTGAA
17582136 GCCAGACCACCAAATCCACCACCTGAAGCAACACCAGAAAACCC
131 GCCAGACCACCAAATCCACCACCTGAAGCAACACCAGAAAACCC
17582180 ACCACCACCTGA
1 ACCACCACCTGA
17582192 AGCCAAACCA
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 185 1.00
ACGTcount: A:0.34, C:0.42, G:0.15, T:0.10
Consensus pattern (174 bp):
ACCACCACCTGAGGCAGGAGCAGCAAATCCTCCAGTACCACCACCAGCAGCTCCAGCAAATCCAC
CACCACCGGAGGCAGAACCTGTAAGTCCTCCACTAGCTAAGCTACCAAATCCCCCACCACCTGAA
GCCAGACCACCAAATCCACCACCTGAAGCAACACCAGAAAACCC
Found at i:17582208 original size:30 final size:30
Alignment explanation
Indices: 17582116--17582212 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
17582106 GCTAAGCTAC
* *
17582116 CAAATCCC-CCACCACCTGAAGCCAGACCAC
1 CAAA-CCCACCACCACCTGAAGCCAAACCAG
*
17582146 CAAA---TCCACCACCTGAAG-CAACACCAG
1 CAAACCCACCACCACCTGAAGCCAA-ACCAG
*
17582173 AAAACCCACCACCACCTGAAGCCAAACCAG
1 CAAACCCACCACCACCTGAAGCCAAACCAG
17582203 CAAACCCACC
1 CAAACCCACC
17582213 TCCTGTTGCA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.04
27 20 0.36
30 31 0.55
31 3 0.05
ACGTcount: A:0.39, C:0.46, G:0.09, T:0.05
Consensus pattern (30 bp):
CAAACCCACCACCACCTGAAGCCAAACCAG
Found at i:17582211 original size:27 final size:27
Alignment explanation
Indices: 17582123--17582217 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 27
17582113 TACCAAATCC
* *
17582123 CCCACCACCTGAAGCCAGACCACCAAA
1 CCCACCACCTGAAGCCAAACCAGCAAA
* *
17582150 TCCACCACCTGAAG-CAACACCAGAAAA
1 CCCACCACCTGAAGCCAA-ACCAGCAAA
17582177 CCCACCACCACCTGAAGCCAAACCAGCAAA
1 --C-CCACCACCTGAAGCCAAACCAGCAAA
*
17582207 CCCACCTCCTG
1 CCCACCACCTG
17582218 TTGCAGCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
26 2 0.04
27 29 0.52
28 1 0.02
30 21 0.38
31 3 0.05
ACGTcount: A:0.37, C:0.46, G:0.11, T:0.06
Consensus pattern (27 bp):
CCCACCACCTGAAGCCAAACCAGCAAA
Found at i:17588861 original size:570 final size:570
Alignment explanation
Indices: 17587782--17589494 Score: 3372
Period size: 570 Copynumber: 3.0 Consensus size: 570
17587772 CCAAGTGGTC
17587782 CAGCTTCACCTACTGGTTCCTTAACCAGCTCAAACTTTTTTGGTATGCTCTCATGGCTGGGTTGT
1 CAGCTTCACCTACTGGTTCCTTAACCAGCTCAAACTTTTTTGGTATGCTCTCATGGCTGGGTTGT
17587847 ATTACGGAGTCATTTGAAACTTTCGCCACAGGAGTAACAGATCCAAATCCTGGAATCTTTTGAGC
66 ATTACGGAGTCATTTGAAACTTTCGCCACAGGAGTAACAGATCCAAATCCTGGAATCTTTTGAGC
17587912 TTCTGTTTGACTACCATCCCTCACCTTGTTATCAGGTCCCTCTAATTGAGAAGTCCTCAGAAATG
131 TTCTGTTTGACTACCATCCCTCACCTTGTTATCAGGTCCCTCTAATTGAGAAGTCCTCAGAAATG
17587977 ATTGTCCTGAATTGGTACCTTGCCCTCCAAAAAACAATTTTTGTTGAGTACCTGCTTCTTGGTAC
196 ATTGTCCTGAATTGGTACCTTGCCCTCCAAAAAACAATTTTTGTTGAGTACCTGCTTCTTGGTAC
*
17588042 AGCATTAAGGTTGGAGGATTTTGTTGGCCCACAGCTTCCGAAGACTGGGAGTTCTTCAAAGATAC
261 AGCATTGAGGTTGGAGGATTTTGTTGGCCCACAGCTTCCGAAGACTGGGAGTTCTTCAAAGATAC
*
17588107 TGCTTTTTTAATATCATCTTTATGGAATAGTTGATCAGTAGCATGTGTAACTGAATTCACCTTCA
326 TGCTTTTTTAATATCATCTTTATGGAATAGTTGATCAGTAGCATGTGTAACTGAATTCACATTCA
17588172 TTTGAGAAAGGTTTACATCACTACTTCCATTGGTGAGAAGCTCAGTTTTGCCTTTATCCATCAAT
391 TTTGAGAAAGGTTTACATCACTACTTCCATTGGTGAGAAGCTCAGTTTTGCCTTTATCCATCAAT
17588237 GGAAGAGACAAAGCTACCAGTTCTGACTTTTGTTCACCCTGTCCATATGTAAGTTCAGGTGGATC
456 GGAAGAGACAAAGCTACCAGTTCTGACTTTTGTTCACCCTGTCCATATGTAAGTTCAGGTGGATC
17588302 AATTTCAGCAGCAGGGGTATCCTCTTCTTTATCAGAAAGGGTAGAAACAT
521 AATTTCAGCAGCAGGGGTATCCTCTTCTTTATCAGAAAGGGTAGAAACAT
17588352 CAGCTTCACCTACTGGTTCCTTAACCAGCTCAAACTTTTTTGGTATGCTCTCATGGCTGGGTTGT
1 CAGCTTCACCTACTGGTTCCTTAACCAGCTCAAACTTTTTTGGTATGCTCTCATGGCTGGGTTGT
17588417 ATTACGGAGTCATTTGAAACTTTCGCCACAGGAGTAACAGATCCAAATCCTGGAATCTTTTGAGC
66 ATTACGGAGTCATTTGAAACTTTCGCCACAGGAGTAACAGATCCAAATCCTGGAATCTTTTGAGC
17588482 TTCTGTTTGACTACCATCCCTCACCTTGTTATCAGGTCCCTCTAATTGAGAAGTCCTCAGAAATG
131 TTCTGTTTGACTACCATCCCTCACCTTGTTATCAGGTCCCTCTAATTGAGAAGTCCTCAGAAATG
17588547 ATTGTCCTGAATTGGTACCTTGCCCTCCAAAAAACAATTTTTGTTGAGTACCTGCTTCTTGGTAC
196 ATTGTCCTGAATTGGTACCTTGCCCTCCAAAAAACAATTTTTGTTGAGTACCTGCTTCTTGGTAC
17588612 AGCATTGAGGTTGGAGGATTTTGTTGGCCCACAGCTTCCGAAGACTGGGAGTTCTTCAAAGATAC
261 AGCATTGAGGTTGGAGGATTTTGTTGGCCCACAGCTTCCGAAGACTGGGAGTTCTTCAAAGATAC
17588677 TGCTTTTTTAATATCATCTTTATGGAATAGTTGATCAGTAGCATGTGTAACTGAATTCACATTCA
326 TGCTTTTTTAATATCATCTTTATGGAATAGTTGATCAGTAGCATGTGTAACTGAATTCACATTCA
17588742 TTTGAGAAAGGTTTACATCACTACTTCCATTGGTGAGAAGCTCAGTTTTGCCTTTATCCATCAAT
391 TTTGAGAAAGGTTTACATCACTACTTCCATTGGTGAGAAGCTCAGTTTTGCCTTTATCCATCAAT
17588807 GGAAGAGACAAAGCTACCAGTTCTGACTTTTGTTCACCCTGTCCATATGTAAGTTCAGGTGGATC
456 GGAAGAGACAAAGCTACCAGTTCTGACTTTTGTTCACCCTGTCCATATGTAAGTTCAGGTGGATC
17588872 AATTTCAGCAGCAGGGGTATCCTCTTCTTTATCAGAAAGGGTAGAAACAT
521 AATTTCAGCAGCAGGGGTATCCTCTTCTTTATCAGAAAGGGTAGAAACAT
17588922 CAGCTTCACCTACTGGTTCCTTAACCAGCTCAAACTTTTTTGGTATGCTCTCATGGCTGGGTTGT
1 CAGCTTCACCTACTGGTTCCTTAACCAGCTCAAACTTTTTTGGTATGCTCTCATGGCTGGGTTGT
17588987 ATTACGGAGTCATTTGAAACTTTCGCCACAGGAGTAACAGATCCAAATCCTGGAATCTTTTGAGC
66 ATTACGGAGTCATTTGAAACTTTCGCCACAGGAGTAACAGATCCAAATCCTGGAATCTTTTGAGC
17589052 TTCTGTTTGACTACCATCCCTCACCTTGTTATCAGGTCCCTCTAATTGAGAAGTCCTCAGAAATG
131 TTCTGTTTGACTACCATCCCTCACCTTGTTATCAGGTCCCTCTAATTGAGAAGTCCTCAGAAATG
* *
17589117 ACTGTCCTGAATTGGTACCTTGCCCTCCAAAATACAATTTTTGTTGAGTACCTGCTTCTTGGTAC
196 ATTGTCCTGAATTGGTACCTTGCCCTCCAAAAAACAATTTTTGTTGAGTACCTGCTTCTTGGTAC
17589182 AGCATTGAGGTTGGAGGATTTTGTTGGCCCACAGCTTCCGAAGACTGGGAGTTCTTCAAAGATAC
261 AGCATTGAGGTTGGAGGATTTTGTTGGCCCACAGCTTCCGAAGACTGGGAGTTCTTCAAAGATAC
17589247 TGCTTTTTTAATATCATCTTTATGGAATAGTTGATCAGTAGCATGTGTAACTGAATTCACATTCA
326 TGCTTTTTTAATATCATCTTTATGGAATAGTTGATCAGTAGCATGTGTAACTGAATTCACATTCA
17589312 TTTGAGAAAGGTTTACATCACTACTTCCATTGGTGAGAAGCTCAGTTTTGCCTTTATCCATCAAT
391 TTTGAGAAAGGTTTACATCACTACTTCCATTGGTGAGAAGCTCAGTTTTGCCTTTATCCATCAAT
*
17589377 GGAAGAGACAAAGCTACCAGTTCGGACTTTTGTTCACCCTGTCCATATGTAAGTTCAGGTGGATC
456 GGAAGAGACAAAGCTACCAGTTCTGACTTTTGTTCACCCTGTCCATATGTAAGTTCAGGTGGATC
*
17589442 AATTTCAGCAGCAGGGGTATCCTCTTCTTTATCAGAAAGGGCAGAAACAT
521 AATTTCAGCAGCAGGGGTATCCTCTTCTTTATCAGAAAGGGTAGAAACAT
17589492 CAG
1 CAG
17589495 GTGGAACATC
Statistics
Matches: 1137, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
570 1137 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (570 bp):
CAGCTTCACCTACTGGTTCCTTAACCAGCTCAAACTTTTTTGGTATGCTCTCATGGCTGGGTTGT
ATTACGGAGTCATTTGAAACTTTCGCCACAGGAGTAACAGATCCAAATCCTGGAATCTTTTGAGC
TTCTGTTTGACTACCATCCCTCACCTTGTTATCAGGTCCCTCTAATTGAGAAGTCCTCAGAAATG
ATTGTCCTGAATTGGTACCTTGCCCTCCAAAAAACAATTTTTGTTGAGTACCTGCTTCTTGGTAC
AGCATTGAGGTTGGAGGATTTTGTTGGCCCACAGCTTCCGAAGACTGGGAGTTCTTCAAAGATAC
TGCTTTTTTAATATCATCTTTATGGAATAGTTGATCAGTAGCATGTGTAACTGAATTCACATTCA
TTTGAGAAAGGTTTACATCACTACTTCCATTGGTGAGAAGCTCAGTTTTGCCTTTATCCATCAAT
GGAAGAGACAAAGCTACCAGTTCTGACTTTTGTTCACCCTGTCCATATGTAAGTTCAGGTGGATC
AATTTCAGCAGCAGGGGTATCCTCTTCTTTATCAGAAAGGGTAGAAACAT
Found at i:17590022 original size:74 final size:74
Alignment explanation
Indices: 17589901--17590048 Score: 226
Period size: 74 Copynumber: 2.0 Consensus size: 74
17589891 AAAAACATTT
* * * *
17589901 GAAAACAAATTCTAAGAATCTTTCAGCACAAAACACAAGATGACACTAT-CTTGTAGGAAATGCC
1 GAAAACAAATTATAAAAATCTTTCAGCACAAAACACAAGATAACACTATAC-TGTAGAAAATGCC
17589965 ACAGTAATTA
65 ACAGTAATTA
* *
17589975 GAAAACAAATTATAAAAATCTTTCAGCATAAAACATAAGATAACACTATACTGTAGAAAATGCCA
1 GAAAACAAATTATAAAAATCTTTCAGCACAAAACACAAGATAACACTATACTGTAGAAAATGCCA
17590040 CAGTAATTA
66 CAGTAATTA
17590049 TGTCTACTAG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 66 0.99
75 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (74 bp):
GAAAACAAATTATAAAAATCTTTCAGCACAAAACACAAGATAACACTATACTGTAGAAAATGCCA
CAGTAATTA
Found at i:17594035 original size:59 final size:59
Alignment explanation
Indices: 17593940--17594056 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
17593930 CTCTTAATGA
* *
17593940 AAGAGTAACTTATTAAGAAGGGAGCTGACACAGAAGAAATGAATATCAGGTGCTACAGT
1 AAGAGTAACTTATTAAGAAGGGAGCTGACACAGAAGAAATGAATATCAGCTGCCACAGT
* *
17593999 AAGAGTACCTTATTAAGAAGGGAGCTGACACTGAAGAAATGAATATCAGCTGCCACAG
1 AAGAGTAACTTATTAAGAAGGGAGCTGACACAGAAGAAATGAATATCAGCTGCCACAG
17594057 AAACCGCAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.20
Consensus pattern (59 bp):
AAGAGTAACTTATTAAGAAGGGAGCTGACACAGAAGAAATGAATATCAGCTGCCACAGT
Found at i:17598412 original size:28 final size:28
Alignment explanation
Indices: 17598372--17598428 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
17598362 AGCAACCCTA
17598372 ACTGGAGTAAAGGTTTCTACCGATACCC
1 ACTGGAGTAAAGGTTTCTACCGATACCC
17598400 ACTGGAGTAAAGGTTTCTACCGATACCC
1 ACTGGAGTAAAGGTTTCTACCGATACCC
17598428 A
1 A
17598429 AATACTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (28 bp):
ACTGGAGTAAAGGTTTCTACCGATACCC
Found at i:17599596 original size:17 final size:16
Alignment explanation
Indices: 17599571--17599605 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17599561 TTAAAAACCC
17599571 AAAAATAAAACAAAAT
1 AAAAATAAAACAAAAT
*
17599587 AAAAATTAAAATAAAAT
1 AAAAA-TAAAACAAAAT
17599604 AA
1 AA
17599606 GCCTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAATAAAACAAAAT
Found at i:17600804 original size:24 final size:24
Alignment explanation
Indices: 17600767--17600823 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
17600757 TGGTTCACTT
* *
17600767 GGTTTAGGTTAAAAAGTTTATAAG
1 GGTTTGGGTCAAAAAGTTTATAAG
*
17600791 GGTTTGGGTCAAAAGGTTTATAAG
1 GGTTTGGGTCAAAAAGTTTATAAG
17600815 GGTTTGGGT
1 GGTTTGGGT
17600824 TTATATGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.02, G:0.33, T:0.37
Consensus pattern (24 bp):
GGTTTGGGTCAAAAAGTTTATAAG
Found at i:17601606 original size:40 final size:39
Alignment explanation
Indices: 17601562--17601763 Score: 224
Period size: 40 Copynumber: 5.1 Consensus size: 39
17601552 TGAGTTTAAA
*
17601562 CACCGGTTCATAGCCTGCTAAGCCGTAGCTTGTATTTTAT
1 CACCGGTT-ATAGCCTGCTAAGCCGTAGCTTGAATTTTAT
* * * *
17601602 CACCGGCTCATAGCCTGCTAAGACGTAGCTTTAACTTTAT
1 CACCGG-TTATAGCCTGCTAAGCCGTAGCTTGAATTTTAT
* *
17601642 CAGCGGCTTATGGCCTGCTAAGCCGTAGCTTGAATTTTAT
1 CACCGG-TTATAGCCTGCTAAGCCGTAGCTTGAATTTTAT
* * * *
17601682 CACTGGCTTAAAGTCTGCTAAGGCGTAGCTTGAATTTTAT
1 CACCGG-TTATAGCCTGCTAAGCCGTAGCTTGAATTTTAT
* * * *
17601722 CACCAGCTTATAGCTTGCTAAGCCGAAGCTTGAACTTTAT
1 CACC-GGTTATAGCCTGCTAAGCCGTAGCTTGAATTTTAT
17601762 CA
1 CA
17601764 AACATAACTT
Statistics
Matches: 135, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
40 133 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (39 bp):
CACCGGTTATAGCCTGCTAAGCCGTAGCTTGAATTTTAT
Found at i:17601709 original size:80 final size:80
Alignment explanation
Indices: 17601571--17601763 Score: 260
Period size: 80 Copynumber: 2.4 Consensus size: 80
17601561 ACACCGGTTC
* * *
17601571 ATAGCCTGCTAAGCCGTAGCTTGTATTTTATCACCGGCTCATAGCCTGCTAAGACGTAGCTTTAA
1 ATAGCCTGCTAAGCCGTAGCTTGAATTTTATCACCGGCTCAAAGCCTGCTAAGACGTAGCTTGAA
* *
17601636 CTTTATCAGCGGCTT
66 CTTTATCACCAGCTT
* * * * *
17601651 ATGGCCTGCTAAGCCGTAGCTTGAATTTTATCACTGGCTTAAAGTCTGCTAAGGCGTAGCTTGAA
1 ATAGCCTGCTAAGCCGTAGCTTGAATTTTATCACCGGCTCAAAGCCTGCTAAGACGTAGCTTGAA
*
17601716 TTTTATCACCAGCTT
66 CTTTATCACCAGCTT
* * *
17601731 ATAGCTTGCTAAGCCGAAGCTTGAACTTTATCA
1 ATAGCCTGCTAAGCCGTAGCTTGAATTTTATCA
17601764 AACATAACTT
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 98 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (80 bp):
ATAGCCTGCTAAGCCGTAGCTTGAATTTTATCACCGGCTCAAAGCCTGCTAAGACGTAGCTTGAA
CTTTATCACCAGCTT
Found at i:17604976 original size:3 final size:3
Alignment explanation
Indices: 17604968--17605000 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
17604958 GCTAGTCGCT
17604968 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17605001 AAGTTGATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17612444 original size:15 final size:15
Alignment explanation
Indices: 17612426--17612464 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
17612416 TTTAGGTCTT
**
17612426 TTAAAATTTTTAAAA
1 TTAAAATTAATAAAA
17612441 TTAAAATTAATAAAA
1 TTAAAATTAATAAAA
*
17612456 GTAAAATTA
1 TTAAAATTA
17612465 CATTTTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAAATTAATAAAA
Found at i:17613068 original size:11 final size:11
Alignment explanation
Indices: 17613046--17613128 Score: 87
Period size: 11 Copynumber: 7.4 Consensus size: 11
17613036 TCTTTGATTT
17613046 TTAAAGTTTAAA
1 TTAAA-TTTAAA
*
17613058 TTAATTTTAAA
1 TTAAATTTAAA
**
17613069 TTTAAATTTATC
1 -TTAAATTTAAA
17613081 TTAAATTTAAA
1 TTAAATTTAAA
* *
17613092 TTTATTTTAAA
1 TTAAATTTAAA
17613103 TTTAAATTT-AA
1 -TTAAATTTAAA
17613114 TTAAATTTAAA
1 TTAAATTTAAA
17613125 TTAA
1 TTAA
17613129 TATTAAACTT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
10 8 0.14
11 32 0.55
12 18 0.31
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:17613072 original size:6 final size:6
Alignment explanation
Indices: 17613045--17613126 Score: 86
Period size: 6 Copynumber: 14.3 Consensus size: 6
17613035 GTCTTTGATT
*
17613045 TTTAAA GTTTAAA -TTAAT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
17613092 TTT-AT TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
17613127 AATATTAAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.06
5 14 0.22
6 38 0.59
7 8 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:17613074 original size:17 final size:17
Alignment explanation
Indices: 17613044--17613140 Score: 117
Period size: 17 Copynumber: 5.7 Consensus size: 17
17613034 AGTCTTTGAT
17613044 TTTTAAAGTTTAAATTAA
1 TTTTAAA-TTTAAATTAA
*
17613062 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTAA
* *
17613079 TCTTAAATTTAAATTTA
1 TTTTAAATTTAAATTAA
17613096 TTTTAAATTTAAATTTAA
1 TTTTAAATTTAAA-TTAA
17613114 --TTAAATTTAAATTAA
1 TTTTAAATTTAAATTAA
* *
17613129 TATTAAACTTAA
1 TTTTAAATTTAA
17613141 TACAAAAATA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
15 4 0.06
16 11 0.15
17 46 0.65
18 10 0.14
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTTAAATTTAAATTAA
Found at i:17613107 original size:23 final size:23
Alignment explanation
Indices: 17613045--17613128 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
17613035 GTCTTTGATT
* *
17613045 TTTAAAGTTTAAATTAATTTTAAA
1 TTTAAA-TTTAACTTAAATTTAAA
*
17613069 TTTAAATTTATCTTAAATTTAAA
1 TTTAAATTTAACTTAAATTTAAA
* *
17613092 TTT-ATTTTAAATTTAAATTT-AA
1 TTTAAATTT-AACTTAAATTTAAA
*
17613114 -TTAAATTTAAATTAA
1 TTTAAATTTAACTTAA
17613129 TATTAAACTT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 8 0.16
22 10 0.20
23 26 0.52
24 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAACTTAAATTTAAA
Found at i:17615148 original size:29 final size:29
Alignment explanation
Indices: 17615080--17615264 Score: 137
Period size: 29 Copynumber: 6.3 Consensus size: 29
17615070 TAGAAATTGT
* * *
17615080 ATTTTGACCCCTAAACTTCTTC-AAAAGTCC
1 ATTTTGACCCCAAAACTTC--CAAAAATTAC
*
17615110 ATTTTGACCCCAAAACTTTCAAAAATTAC
1 ATTTTGACCCCAAAACTTCCAAAAATTAC
* ** * *
17615139 ATTTTTACCCCCGAACTTCCAAAATTTCC
1 ATTTTGACCCCAAAACTTCCAAAAATTAC
* *
17615168 ATTTTGACCTCAAAACTTCCAAAAATTTC
1 ATTTTGACCCCAAAACTTCCAAAAATTAC
* * *
17615197 ATTTTTGATCCC-GAACTTCAAAAAATT-C
1 A-TTTTGACCCCAAAACTTCCAAAAATTAC
* *
17615225 AATTTTTGACCCCTAAAC-TCCTAAAATTACC
1 -A-TTTTGACCCCAAAACTTCCAAAAATTA-C
17615256 ATTTT-ACCC
1 ATTTTGACCC
17615265 TCGGATGTTC
Statistics
Matches: 125, Mismatches: 24, Indels: 14
0.77 0.15 0.09
Matches are distributed among these distances:
28 6 0.05
29 89 0.71
30 29 0.23
31 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
ATTTTGACCCCAAAACTTCCAAAAATTAC
Found at i:17615191 original size:58 final size:58
Alignment explanation
Indices: 17615102--17615264 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 58
17615092 AAACTTCTTC
* * *
17615102 AAAAGTCCATTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACTTCAA
* * * *
17615160 AAATTTCCATTTTGACCTCAAAACTTCCAAAAATTTCATTTTTGA-TCCCGAACTTCAA
1 AAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACATTTTT-ACCCCCGAACTTCAA
* * *
17615218 AAAATTCAATTTTTGACCCCTAAAC-TCCTAAAATTACCA-TTTTACCC
1 AAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTA-CATTTTTACCC
17615265 TCGGATGTTC
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
57 1 0.01
58 70 0.80
59 16 0.18
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACTTCAA
Found at i:17615222 original size:87 final size:86
Alignment explanation
Indices: 17615127--17615346 Score: 209
Period size: 87 Copynumber: 2.5 Consensus size: 86
17615117 CCCCAAAACT
17615127 TTCAAAAATTACATTTTTACCCCCGAACTTCCAAAATTTCCATTTTGA-CCTCAAAACTTCCAAA
1 TTCAAAAATTACATTTTTACCCCCGAACTTCCAAAATTTCCATTTT-ACCCTCAAAACTT-CAAA
17615191 AATTTCATTTTTGATCCCGA-AC
64 AATTTCATTTTTGATCCCGATAC
** * ** **
17615213 TTCAAAAAATT-CAATTTTTGACCCCTAAAC-TCCTAAAATTACCATTTTACCCTCGGATGTTCA
1 TTC-AAAAATTAC-ATTTTT-ACCCCCGAACTTCC-AAAATTTCCATTTTACCCTCAAAACTTCA
* *
17615276 AAAATTTCGTTTTTGATCCCGATTC
62 AAAATTTCATTTTTGATCCCGATAC
* * * *
17615301 TTCTAAAATTACCA-TTTTACCCTCGAA-TGTCCAAAAATTCCGTTTT
1 TTCAAAAATTA-CATTTTTACCCCCGAACT-TCCAAAATTTCCATTTT
17615347 TAATCTCTAT
Statistics
Matches: 108, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
86 21 0.19
87 53 0.49
88 33 0.31
89 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (86 bp):
TTCAAAAATTACATTTTTACCCCCGAACTTCCAAAATTTCCATTTTACCCTCAAAACTTCAAAAA
TTTCATTTTTGATCCCGATAC
Found at i:17615279 original size:29 final size:29
Alignment explanation
Indices: 17615247--17615469 Score: 123
Period size: 29 Copynumber: 7.6 Consensus size: 29
17615237 CTAAACTCCT
*
17615247 AAAATTACCATTTTACCCTCGGATGTTCA
1 AAAATTACCATTTTACCCTCGAATGTTCA
* ** * * * *
17615276 AAAATTTCGTTTTTGATCC-CGATTCTTCT
1 AAAATTACCATTTT-ACCCTCGAATGTTCA
*
17615305 AAAATTACCATTTTACCCTCGAATGTCCA
1 AAAATTACCATTTTACCCTCGAATGTTCA
* ** * * *
17615334 AAAATT-CCGTTTTTAATCTCTATTTTTCCAAA
1 AAAATTACC-ATTTTACCCTCGAATGTT-C--A
*
17615366 AAAATTACCATTTTACCCTCGAATGTCCA
1 AAAATTACCATTTTACCCTCGAATGTTCA
* * * *
17615395 AAAAGT--CATTTTAACCC-CAAATTTTCCC
1 AAAATTACCATTTT-ACCCTCGAATGTT-CA
* * * * *
17615423 AAAATTACCATTTTGCCCTCAAAAGTCCC
1 AAAATTACCATTTTACCCTCGAATGTTCA
17615452 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
17615470 CTGGGTATCC
Statistics
Matches: 141, Mismatches: 41, Indels: 24
0.68 0.20 0.12
Matches are distributed among these distances:
27 11 0.08
28 15 0.11
29 79 0.56
30 15 0.11
31 1 0.01
32 18 0.13
33 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAATGTTCA
Found at i:17615281 original size:58 final size:57
Alignment explanation
Indices: 17615217--17615457 Score: 171
Period size: 58 Copynumber: 4.1 Consensus size: 57
17615207 CCGAACTTCA
* * *
17615217 AAAAATTCAATTTTTGACCCCTAAACTCCTAAAATTACCATTTTACCCTCGGATGTTC
1 AAAAATTC-ATTTTTGACCCCGAAACTCCTAAAATTACCATTTTACCCTCGAATGTCC
* * ** *
17615275 AAAAATTTCGTTTTTGATCCCGATTCTTCTAAAATTACCATTTTACCCTCGAATGTCC
1 AAAAA-TTCATTTTTGACCCCGAAACTCCTAAAATTACCATTTTACCCTCGAATGTCC
* * * * * *** *
17615333 AAAAATTCCGTTTTTAATCTCTATTTTTCCAAAAAAATTACCATTTTACCCTCGAATGTCC
1 AAAAATT-CATTTTTGACCCCGA-AACTCC--TAAAATTACCATTTTACCCTCGAATGTCC
* * * * * * *
17615394 AAAAAGTCA-TTTTAACCCC-AAATTTTCCCAAAATTACCATTTTGCCCTCAAAAGTCC
1 AAAAATTCATTTTTGACCCCGAAA--CTCCTAAAATTACCATTTTACCCTCGAATGTCC
*
17615451 CAAAATT
1 AAAAATT
17615458 ACCATTTTAC
Statistics
Matches: 150, Mismatches: 26, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
57 32 0.21
58 64 0.43
59 19 0.13
60 1 0.01
61 34 0.23
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (57 bp):
AAAAATTCATTTTTGACCCCGAAACTCCTAAAATTACCATTTTACCCTCGAATGTCC
Found at i:17615383 original size:61 final size:58
Alignment explanation
Indices: 17615247--17615398 Score: 205
Period size: 58 Copynumber: 2.6 Consensus size: 58
17615237 CTAAACTCCT
* * * * *
17615247 AAAATTACCATTTTACCCTCGGATGTTCAAAAATTTCGTTTTTGATCCCGATTCTTCT
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCGTTTTTAATCCCGATTCTTCA
* * *
17615305 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCGTTTTTAATCTCTATTTTTCCAAA
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCGTTTTTAATCCCGATTCTT-C--A
17615366 AAAATTACCATTTTACCCTCGAATGTCCAAAAA
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAA
17615399 GTCATTTTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
58 49 0.59
59 1 0.01
61 33 0.40
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCGTTTTTAATCCCGATTCTTCA
Found at i:17627332 original size:92 final size:92
Alignment explanation
Indices: 17627165--17627988 Score: 1416
Period size: 92 Copynumber: 9.0 Consensus size: 92
17627155 AGATCAAAAT
*
17627165 AACAACAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* * *
17627230 TTGTAATAAGAGTAAGATAAAG-ATTCA
66 TTGTAGTAAGAGCAAGATGAAGCA-TCA
* * * *
17627257 AACATCATTTCCTATCCTCTTGAAATTGTAGTAAAGTTGGACAGCAAGTCTTTATCTCTCTAAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
17627322 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * *
17627349 AACATCAATTCCTATCCTCTTGAAGTTGTATTGATGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
17627414 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
*
17627441 AACATCAATTCTTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
17627506 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
**
17627533 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAATAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
17627598 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
*
17627625 AACATCAATTTCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
17627690 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
17627717 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
*
17627782 TCGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
**
17627809 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCCCAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
**
17627874 TTGTAGTAAGAGCAAGATGAAGTTTCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
17627901 AACATCAATTCTTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTCATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* *
17627966 TTGTAGTAGGAGTAAGATGAAGC
66 TTGTAGTAAGAGCAAGATGAAGC
17627989 CACGACATCA
Statistics
Matches: 692, Mismatches: 39, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
92 691 1.00
93 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (92 bp):
AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
TTGTAGTAAGAGCAAGATGAAGCATCA
Found at i:17628274 original size:17 final size:17
Alignment explanation
Indices: 17628244--17628290 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
17628234 GGCCTTTGAT
17628244 TTTTAAAGTTTAAATTAA
1 TTTTAAA-TTTAAATTAA
17628262 TTTTAAATTTAAATTAA
1 TTTTAAATTTAAATTAA
*
17628279 TATTAAATTTAA
1 TTTTAAATTTAA
17628291 TACAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTTAAATTTAAATTAA
Found at i:17630299 original size:29 final size:29
Alignment explanation
Indices: 17630213--17630477 Score: 201
Period size: 29 Copynumber: 9.0 Consensus size: 29
17630203 GAAGGTCCTT
* * * *
17630213 AAACTATCTAGAAATTGTATTTTGACCCCC
1 AAACT-TCTAAAAATTATATTTTAACCCCG
* * *
17630243 AAACTTCTTCAAAATTATATTTTGACCTCG
1 AAACTTC-TAAAAATTATATTTTAACCCCG
*
17630273 AAACTTCTAAAAATTATATTTTAACCTCG
1 AAACTTCTAAAAATTATATTTTAACCCCG
* * * *
17630302 AAACTTCCAAAAATTACATTTTTAACCTCA
1 AAACTTCTAAAAATTATA-TTTTAACCCCG
* * * *
17630332 AAACTTCAAAAAATTACATTTTTACCCCT
1 AAACTTCTAAAAATTATATTTTAACCCCG
* **
17630361 AAACTTCTAAAAATTATATTTTTACCCTT
1 AAACTTCTAAAAATTATATTTTAACCCCG
* * **
17630390 AAACTTCCAAAAAGTT-CATTTTAACCCTA
1 AAACTTCTAAAAA-TTATATTTTAACCCCG
* * *
17630419 AAACTTCCAAAAATTCAAATTTTGACCCCG
1 AAACTTCTAAAAATT-ATATTTTAACCCCG
* * *
17630449 AAACTCCT-AAAATTACCATTTTACCCCCG
1 AAACTTCTAAAAATTA-TATTTTAACCCCG
17630478 GATGTCCAAA
Statistics
Matches: 199, Mismatches: 30, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.02
29 123 0.62
30 73 0.37
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTTCTAAAAATTATATTTTAACCCCG
Found at i:17630306 original size:59 final size:58
Alignment explanation
Indices: 17630213--17630476 Score: 221
Period size: 59 Copynumber: 4.5 Consensus size: 58
17630203 GAAGGTCCTT
* ** * *
17630213 AAACTATCTAGAAATTGTATTTTGACCCCCAAACTTCTTC-AAAATTATATTTTGACCTCG
1 AAACT-TCTAAAAATTACATTTTAACCCCAAAACTTC--CAAAAATTATATTTTGACCTCG
* * * * * *
17630273 AAACTTCTAAAAATTATATTTTAACCTCGAAACTTCCAAAAATTACATTTTTAACCTCA
1 AAACTTCTAAAAATTACATTTTAACCCCAAAACTTCCAAAAATTATA-TTTTGACCTCG
* * * * * *
17630332 AAACTTCAAAAAATTACATTTTTACCCCTAAACTTCTAAAAATTATATTTTTACC-CTT
1 AAACTTCTAAAAATTACATTTTAACCCCAAAACTTCCAAAAATTATATTTTGACCTC-G
* * * *
17630390 AAACTTCCAAAAAGTT-CATTTTAACCCTAAAACTTCCAAAAATTCAAATTTTGACCCCG
1 AAACTTCTAAAAA-TTACATTTTAACCCCAAAACTTCCAAAAATT-ATATTTTGACCTCG
* *
17630449 AAACTCCT-AAAATTACCATTTTACCCCC
1 AAACTTCTAAAAATTA-CATTTTAACCCC
17630477 GGATGTCCAA
Statistics
Matches: 167, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
57 4 0.02
58 55 0.33
59 102 0.61
60 6 0.04
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTCTAAAAATTACATTTTAACCCCAAAACTTCCAAAAATTATATTTTGACCTCG
Found at i:17630470 original size:88 final size:88
Alignment explanation
Indices: 17630253--17630474 Score: 274
Period size: 88 Copynumber: 2.5 Consensus size: 88
17630243 AAACTTCTTC
* * *
17630253 AAAATTATATTTTGACCTCGAAACTTCTAAAAATTATATTTTAACCTCGAAACTTCCAAAAATTA
1 AAAATTAAATTTTGACCCCGAAACTTCTAAAAATTATATTTTACCCTCGAAACTTCCAAAAATTA
17630318 CATTTTTAACCTCAAAACTTCAA
66 CATTTTTAACCTCAAAACTTCAA
* * * *
17630341 AAAATTACATTTTTACCCCTAAACTTCTAAAAATTATATTTTTACCCT-TAAACTTCCAAAAAGT
1 AAAATTAAATTTTGACCCCGAAACTTCTAAAAATTATA-TTTTACCCTCGAAACTTCCAAAAA-T
*
17630405 T-CA-TTTTAACC-CTAAAACTTCCA
64 TACATTTTTAACCTC-AAAACTTCAA
* *
17630428 AAAATTCAAATTTTGACCCCGAAACTCCT-AAAATTACCATTTTACCC
1 AAAATT-AAATTTTGACCCCGAAACTTCTAAAAATTA-TATTTTACCC
17630475 CCGGATGTCC
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
86 1 0.01
87 38 0.32
88 68 0.58
89 10 0.09
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.35
Consensus pattern (88 bp):
AAAATTAAATTTTGACCCCGAAACTTCTAAAAATTATATTTTACCCTCGAAACTTCCAAAAATTA
CATTTTTAACCTCAAAACTTCAA
Found at i:17630500 original size:58 final size:58
Alignment explanation
Indices: 17630424--17630559 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 58
17630414 CCCTAAAACT
*
17630424 TCCAAAAATTCAAATTTTGACCCCGAAACTCCTAAAATTACCATTTTACCCCCGGATG
1 TCCAAAAATTCAATTTTTGACCCCGAAACTCCTAAAATTACCATTTTACCCCCGGATG
** * * *** * ***
17630482 TCCAAAAATTCTGTTTTTGATCTCGGTTCTTCTAAAATTACCATTTTACCTTTGGATG
1 TCCAAAAATTCAATTTTTGACCCCGAAACTCCTAAAATTACCATTTTACCCCCGGATG
* *
17630540 TCTAAAAATTCCATTTTTGA
1 TCCAAAAATTCAATTTTTGA
17630560 TCCTGATTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (58 bp):
TCCAAAAATTCAATTTTTGACCCCGAAACTCCTAAAATTACCATTTTACCCCCGGATG
Found at i:17630663 original size:29 final size:29
Alignment explanation
Indices: 17630631--17630686 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
17630621 CCCCGAATTT
*
17630631 TCCCAAAGTTACCATTTTACCCCCGAGAG
1 TCCCAAAATTACCATTTTACCCCCGAGAG
* * *
17630660 TCCCAAAATTATCATTTTGCCCTCGAG
1 TCCCAAAATTACCATTTTACCCCCGAG
17630687 TATCCAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (29 bp):
TCCCAAAATTACCATTTTACCCCCGAGAG
Found at i:17643338 original size:21 final size:21
Alignment explanation
Indices: 17643314--17643359 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17643304 GACGCATTTT
17643314 TTTTATTT-TCTTT-CTATTTAC
1 TTTTATTTGT-TTTACT-TTTAC
17643335 TTTTATTTGTTTTACTTTTAC
1 TTTTATTTGTTTTACTTTTAC
17643356 TTTT
1 TTTT
17643360 GTTGTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATTTGTTTTACTTTTAC
Found at i:17645686 original size:17 final size:18
Alignment explanation
Indices: 17645664--17645703 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
17645654 ATAGTTTTCA
*
17645664 TGCATTTT-TATTGTCAT
1 TGCATTTTATATTGTCAC
*
17645681 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
17645699 TGCAT
1 TGCAT
17645704 CCCTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:17649093 original size:12 final size:12
Alignment explanation
Indices: 17649076--17649115 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
17649066 GCTCCTTCGC
17649076 TTTTCTTTCTTG
1 TTTTCTTTCTTG
17649088 TTTTCTTTCTTG
1 TTTTCTTTCTTG
17649100 -TTTCTTTTCTTG
1 TTTTC-TTTCTTG
17649112 TTTT
1 TTTT
17649116 GTTTGCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.15
12 19 0.73
13 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTCTTTCTTG
Found at i:17656130 original size:21 final size:21
Alignment explanation
Indices: 17656097--17656138 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17656087 ACACTTGGTA
*
17656097 AAAGGCATTGATACTTTTTGT
1 AAAGGCATCGATACTTTTTGT
* *
17656118 AAAGGTATCGATATTTTTTGT
1 AAAGGCATCGATACTTTTTGT
17656139 GATTGTTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (21 bp):
AAAGGCATCGATACTTTTTGT
Found at i:17656203 original size:18 final size:19
Alignment explanation
Indices: 17656169--17656204 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17656159 AAAGAAAAAG
17656169 AAAATGTGGTATCGATATT
1 AAAATGTGGTATCGATATT
*
17656188 AAAATG-GGTATTGATAT
1 AAAATGTGGTATCGATAT
17656205 CTTGAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (19 bp):
AAAATGTGGTATCGATATT
Found at i:17656327 original size:20 final size:18
Alignment explanation
Indices: 17656280--17656329 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
17656270 GTTTTAAAAT
* *
17656280 AATTTTAACATGATTGAA
1 AATTTTAACTTAATTGAA
17656298 AATGTTTAACTTAATTGAA
1 AAT-TTTAACTTAATTGAA
17656317 ACCATTTTAACTT
1 A--ATTTTAACTT
17656330 GATTTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 14 0.52
20 8 0.30
21 2 0.07
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (18 bp):
AATTTTAACTTAATTGAA
Found at i:17656531 original size:30 final size:30
Alignment explanation
Indices: 17656482--17656541 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17656472 TTTTTGAATA
* *
17656482 AATTGCTCCATCTTAATAAAAGTCTTTTTC
1 AATTGCTCCATCTTAATAAAAATCATTTTC
*
17656512 AATTGCTCCCTC-TATATAAAAATCATTTTC
1 AATTGCTCCATCTTA-ATAAAAATCATTTTC
17656542 TATTTAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (30 bp):
AATTGCTCCATCTTAATAAAAATCATTTTC
Found at i:17666352 original size:26 final size:26
Alignment explanation
Indices: 17666316--17666522 Score: 190
Period size: 26 Copynumber: 8.0 Consensus size: 26
17666306 ATAATTACCA
*
17666316 GCTCGAAGCCTGCTAATTATTCATCG
1 GCTCGAAGCCTGCTAATTATTCACCG
*
17666342 GCTCGAAGCCTGCTATTTATTCACCG
1 GCTCGAAGCCTGCTAATTATTCACCG
* *
17666368 GCTC-AAGGCTTGTTAATTATTCACCG
1 GCTCGAA-GCCTGCTAATTATTCACCG
* *
17666394 GCTC-AAGGCCT-ATTATATATTCACCG
1 GCTCGAA-GCCTGCTAAT-TATTCACCG
* * * **
17666420 ACTTGAAGCCTGCTATTTATTCATTG
1 GCTCGAAGCCTGCTAATTATTCACCG
* *
17666446 GCTC-AAGGCCTGCT-ATATACTCACTG
1 GCTCGAA-GCCTGCTAAT-TATTCACCG
*
17666472 GCTCGAAGCCTGCTAATTATTCACAG
1 GCTCGAAGCCTGCTAATTATTCACCG
* *
17666498 GCTCGAAGCGTGCTATTTATTCACC
1 GCTCGAAGCCTGCTAATTATTCACC
17666523 AGCTTAAGGG
Statistics
Matches: 148, Mismatches: 25, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
25 8 0.05
26 132 0.89
27 8 0.05
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (26 bp):
GCTCGAAGCCTGCTAATTATTCACCG
Found at i:17666475 original size:78 final size:78
Alignment explanation
Indices: 17666302--17666544 Score: 242
Period size: 78 Copynumber: 3.1 Consensus size: 78
17666292 ACAAAGTCTA
* * * * *
17666302 CTATATAATTACCAGCTCGAAGCCTGCTAATTATTCATC-GGCTCGAAGCCTGCTATTTATTCAC
1 CTATATACTCACCGGCTCGAAGCCTACTAATTATTCA-CAGACTCGAAGCCTGCTATTTATTCAC
*
17666366 CGGCTCAAGGCTTG
65 CGGCTCAAGGCCTG
* * * * *
17666380 TTA-ATTATTCACCGGCTC-AAGGCCTA-TTATATATTCACCGACTTGAAGCCTGCTATTTATTC
1 CTATA-TACTCACCGGCTCGAA-GCCTACTAAT-TATTCACAGACTCGAAGCCTGCTATTTATTC
**
17666442 ATTGGCTCAAGGCCTG
63 ACCGGCTCAAGGCCTG
* * * *
17666458 CTATATACTCACTGGCTCGAAGCCTGCTAATTATTCACAGGCTCGAAGCGTGCTATTTATTCACC
1 CTATATACTCACCGGCTCGAAGCCTACTAATTATTCACAGACTCGAAGCCTGCTATTTATTCACC
* * *
17666523 AGCTTAAGGGCTG
66 GGCTCAAGGCCTG
17666536 CTATATACT
1 CTATATACT
17666545 TGTTTACGAT
Statistics
Matches: 133, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
77 7 0.05
78 120 0.90
79 6 0.05
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (78 bp):
CTATATACTCACCGGCTCGAAGCCTACTAATTATTCACAGACTCGAAGCCTGCTATTTATTCACC
GGCTCAAGGCCTG
Found at i:17671582 original size:16 final size:16
Alignment explanation
Indices: 17671558--17671589 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17671548 TACTTACAAA
*
17671558 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
17671574 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
17671590 AAAAATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:17672124 original size:20 final size:19
Alignment explanation
Indices: 17672071--17672125 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
17672061 TTTCAACTTT
17672071 TGCACCTTTTACGATTTAA
1 TGCACCTTTTACGATTTAA
*
17672090 T---CCTTTTTC-ATTTAA
1 TGCACCTTTTACGATTTAA
17672105 TAGCACCTTTTACGATTTAA
1 T-GCACCTTTTACGATTTAA
17672125 T
1 T
17672126 CCTAATGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 7 0.24
16 7 0.24
19 8 0.28
20 7 0.24
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (19 bp):
TGCACCTTTTACGATTTAA
Done.