Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008958.1 Hibiscus syriacus cultivar Beakdansim tig00112289_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2490255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:4610 original size:30 final size:28
Alignment explanation
Indices: 4576--4632 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
4566 AATACTTGCA
*
4576 AATAAATAAACATATAAATATTATGAAAAT
1 AATAAAT-AA-ATATAAAAATTATGAAAAT
* *
4606 AATAAGTAAATATAAAAATTTTGAAAA
1 AATAAATAAATATAAAAATTATGAAAA
4633 GAAAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
29 2 0.08
30 6 0.25
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (28 bp):
AATAAATAAATATAAAAATTATGAAAAT
Found at i:5423 original size:48 final size:45
Alignment explanation
Indices: 5330--5424 Score: 102
Period size: 48 Copynumber: 2.0 Consensus size: 45
5320 AAAAATATTT
* * *
5330 AACAATATATAAATAAAAATACAAATACTACTAAAATATATTAAA
1 AACAATAAATAAATAAAAATACAAATACTACTAAAATACAATAAA
* *
5375 AACAATAAAT-AATGAAAACATATAAATAACTGACTAAATTACAATAAA
1 AACAATAAATAAAT-AAAA-ATACAAAT-ACT-ACTAAAATACAATAAA
5423 AA
1 AA
5425 TAAAATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
44 3 0.07
45 13 0.32
46 7 0.17
47 3 0.07
48 15 0.37
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (45 bp):
AACAATAAATAAATAAAAATACAAATACTACTAAAATACAATAAA
Found at i:6243 original size:21 final size:21
Alignment explanation
Indices: 6218--6265 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
6208 GTTTGTATCT
*
6218 TCTCTGTTTTTTTTTTCTGTC
1 TCTCTGTCTTTTTTTTCTGTC
6239 TCTC--TCTTTTTTTTCTGTC
1 TCTCTGTCTTTTTTTTCTGTC
6258 TCTCTGTC
1 TCTCTGTC
6266 CCGTTCTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 18 0.75
21 6 0.25
ACGTcount: A:0.00, C:0.25, G:0.08, T:0.67
Consensus pattern (21 bp):
TCTCTGTCTTTTTTTTCTGTC
Found at i:6248 original size:19 final size:19
Alignment explanation
Indices: 6226--6262 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6216 CTTCTCTGTT
6226 TTTTTTTTCTGTCTCTCTC
1 TTTTTTTTCTGTCTCTCTC
6245 TTTTTTTTCTGTCTCTCT
1 TTTTTTTTCTGTCTCTCT
6263 GTCCCGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTTTTTCTGTCTCTCTC
Found at i:6730 original size:11 final size:11
Alignment explanation
Indices: 6701--6738 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6691 AATTGGTCTG
6701 TAAT-TATATT
1 TAATATATATT
*
6711 TATATATATGTT
1 TA-ATATATATT
6723 TAATATATATT
1 TAATATATATT
6734 TAATA
1 TAATA
6739 ATAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 2 0.08
11 15 0.62
12 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATATATT
Found at i:6742 original size:3 final size:3
Alignment explanation
Indices: 6734--6802 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
6724 AATATATATT
6734 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
6780 TAT TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
6803 TGGATAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 56 0.93
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:6817 original size:32 final size:32
Alignment explanation
Indices: 6736--6820 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 32
6726 TATATATTTA
6736 ATAATAATAATAATAA-TAATA-TAATAATAAT
1 ATAATAATAATAA-AATTAATATTAATAATAAT
*
6767 ATAATAATAATAATATTAATATTAATAATAAT
1 ATAATAATAATAAAATTAATATTAATAATAAT
*
6799 A-ATATGGATAA-AAAATTAATAT
1 ATA-AT-AATAATAAAATTAATAT
6821 CTTCATATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 1 0.02
31 19 0.40
32 23 0.49
33 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (32 bp):
ATAATAATAATAAAATTAATATTAATAATAAT
Found at i:11042 original size:13 final size:13
Alignment explanation
Indices: 11024--11053 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
11014 TTCCGTTCAC
11024 TTTTGTTGAAACA
1 TTTTGTTGAAACA
11037 TTTTGTTGAAACA
1 TTTTGTTGAAACA
11050 TTTT
1 TTTT
11054 AATATTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTTGTTGAAACA
Found at i:11103 original size:30 final size:30
Alignment explanation
Indices: 11069--11129 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
11059 TTCGATATAA
*
11069 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
11099 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
11129 C
1 C
11130 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:17219 original size:23 final size:21
Alignment explanation
Indices: 17166--17228 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
17156 TTTTGGTGCA
*
17166 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
17187 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
17208 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
17229 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:17236 original size:21 final size:21
Alignment explanation
Indices: 17168--17249 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
17158 TTGGTGCAGA
* *
17168 GGGAATCGATTCCCCCC-CTG
1 GGGAACCGATTCCCCCCACAG
*
17188 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
17212 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
17233 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
17250 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 32 0.64
23 16 0.32
24 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:19650 original size:75 final size:75
Alignment explanation
Indices: 19522--19677 Score: 294
Period size: 75 Copynumber: 2.1 Consensus size: 75
19512 AATAAGTGCT
*
19522 AAATGTTTTACATAATAAATTGAAGTTGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTT
1 AAAT-TTTTACATAATAAATTGAAGTGGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTT
19587 CAAAAATCTTA
65 CAAAAATCTTA
19598 AAATTTTTACATAATAAATTGAAGTGGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTC
1 AAATTTTTACATAATAAATTGAAGTGGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTC
19663 AAAAATCTTA
66 AAAAATCTTA
19673 AAATT
1 AAATT
19678 ACTAAAATGT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 75 0.95
76 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (75 bp):
AAATTTTTACATAATAAATTGAAGTGGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTC
AAAAATCTTA
Found at i:19730 original size:13 final size:13
Alignment explanation
Indices: 19712--19739 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19702 AAGGGGGAGA
19712 TTGTTGAAACATT
1 TTGTTGAAACATT
19725 TTGTTGAAACATT
1 TTGTTGAAACATT
19738 TT
1 TT
19740 AATATTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTGTTGAAACATT
Found at i:19789 original size:30 final size:30
Alignment explanation
Indices: 19755--19815 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
19745 TTCGATATAA
*
19755 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
19785 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
19815 C
1 C
19816 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:20852 original size:36 final size:36
Alignment explanation
Indices: 20812--20991 Score: 265
Period size: 36 Copynumber: 5.0 Consensus size: 36
20802 TAACTCAACA
*
20812 ACTTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC
1 ACTTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
* *
20848 ACTTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC
1 ACTTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
*
20884 -TTCTTGAATCGAAAGTGCCGATGCTTCCTTCCGTT-
1 ACT-TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
* *
20919 ATTCTTGAATCGAAAGTGCTGATGCTTCCTTCCGTTC
1 ACT-TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
*
20956 ACTTTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC
1 ACTTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
20992 TTCTTTCTCA
Statistics
Matches: 133, Mismatches: 8, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
35 1 0.01
36 130 0.98
37 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (36 bp):
ACTTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
Found at i:22249 original size:20 final size:20
Alignment explanation
Indices: 22224--22267 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
22214 CAGACTTTGT
*
22224 AACTAAACATTAACAACCTC
1 AACTAAACATAAACAACCTC
*
22244 AACTAAACATAAACAACCTT
1 AACTAAACATAAACAACCTC
22264 AACT
1 AACT
22268 GTTAACAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.20
Consensus pattern (20 bp):
AACTAAACATAAACAACCTC
Found at i:32269 original size:20 final size:20
Alignment explanation
Indices: 32246--32322 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
32236 CACGGAATGT
32246 AAGATTACCAATGGGAATAA
1 AAGATTACCAATGGGAATAA
*
32266 AAGATTACCAGTGGGAATAA
1 AAGATTACCAATGGGAATAA
* *
32286 AAGATTACTAGTGGGAATAA
1 AAGATTACCAATGGGAATAA
32306 AAGATTA-CAA-GGGAATA
1 AAGATTACCAATGGGAATA
32323 GGATTACTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.13
19 1 0.02
20 45 0.85
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (20 bp):
AAGATTACCAATGGGAATAA
Found at i:37080 original size:34 final size:34
Alignment explanation
Indices: 37041--37125 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
37031 CAATTATATA
37041 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
37075 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
37109 TATATATAAAATATTTT
1 TATATATATAATATTTT
37126 CGGGTCGAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:38702 original size:29 final size:27
Alignment explanation
Indices: 38656--38719 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
38646 TTGATAACAA
*
38656 TAAACTCTAAACTATAACCTCATAACATT
1 TAAACCCTAAACTATAACC-CATAAC-TT
*
38685 TAAACCCTAAACCT-TAACCCCTAACTT
1 TAAACCCTAAA-CTATAACCCATAACTT
*
38712 AAAACCCT
1 TAAACCCT
38720 CAATTTAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 9 0.29
28 5 0.16
29 15 0.48
30 2 0.06
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (27 bp):
TAAACCCTAAACTATAACCCATAACTT
Found at i:43924 original size:25 final size:25
Alignment explanation
Indices: 43896--43961 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
43886 CATACTAAGG
43896 GAGAGTTTTGTGGTGGTGAAGAAAT
1 GAGAGTTTTGTGGTGGTGAAGAAAT
*
43921 GAGAGTTTTATGGTGGTGAAGAAAT
1 GAGAGTTTTGTGGTGGTGAAGAAAT
*
43946 GGGAGTTTTGTGGTGG
1 GAGAGTTTTGTGGTGG
43962 CAAATCTCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (25 bp):
GAGAGTTTTGTGGTGGTGAAGAAAT
Found at i:44890 original size:66 final size:65
Alignment explanation
Indices: 44784--44916 Score: 203
Period size: 66 Copynumber: 2.0 Consensus size: 65
44774 TAATGGAAAA
44784 AAATTAAACGCGTGACCTTCTCCTCCTTTCTCCCTTTCTTTTTCCCCTTGTTTAGTTCCAATAAT
1 AAATTAAACGCGTGACCTTCTCCTCCTTTCTCCCTTTCTTTTT-CCCTTGTTTAGTTCCAATAAT
44849 C
65 C
* ** * * *
44850 AAATTAAACGGGTGATTTTCTCCTCCTTTCTTCCTTTCTTTTTCCTTTTTTTAGTTCCAATAATC
1 AAATTAAACGCGTGACCTTCTCCTCCTTTCTCCCTTTCTTTTTCCCTTGTTTAGTTCCAATAATC
44915 AA
1 AA
44917 CACACATGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
65 22 0.36
66 39 0.64
ACGTcount: A:0.20, C:0.27, G:0.08, T:0.46
Consensus pattern (65 bp):
AAATTAAACGCGTGACCTTCTCCTCCTTTCTCCCTTTCTTTTTCCCTTGTTTAGTTCCAATAATC
Found at i:49800 original size:36 final size:36
Alignment explanation
Indices: 49724--50067 Score: 449
Period size: 36 Copynumber: 9.6 Consensus size: 36
49714 AAAGACGAAC
* * * * * *
49724 ACTTGAAACGAAAGTG-CGATACATCATTCCATTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
**
49759 ACTTGAATCGGAAGTGTTGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
49795 ACTTGAATAGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
** * * *
49831 ACTTGAATATGAAGTGACGGTTCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
49867 ACTTGAATCGGAAGTGCCGATACTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* ** *
49903 ACTTGAATCGGAAGCGGTGATGCTTCCTTTCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
49939 ACTTGAATCGGAAGCGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * * *
49975 ACTTGAATCGAAAGCGTCGATGCTTCATTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
50011 ACTTGAATCGGAAGCGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
50047 ACTTGAATCGGAAGTG-CGATG
1 ACTTGAATCGGAAGTGCCGATG
50068 TTTTCTTTTG
Statistics
Matches: 274, Mismatches: 34, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 19 0.07
36 255 0.93
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:51067 original size:12 final size:12
Alignment explanation
Indices: 51050--51079 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
51040 AAGAATAAGT
51050 GGTTCCGAGATC
1 GGTTCCGAGATC
51062 GGTTCCGAGATC
1 GGTTCCGAGATC
*
51074 GATTCC
1 GGTTCC
51080 AATAGCTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (12 bp):
GGTTCCGAGATC
Found at i:53885 original size:28 final size:27
Alignment explanation
Indices: 53837--53890 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
53827 ATTTTTAAAA
53837 AAAACATTTTTGAAAATATATAATATT
1 AAAACATTTTTGAAAATATATAATATT
53864 AAAACA-TTTTGAAAACTTATATAATAT
1 AAAACATTTTTGAAAA--TATATAATAT
53891 ATAGTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.36
27 6 0.24
28 10 0.40
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (27 bp):
AAAACATTTTTGAAAATATATAATATT
Found at i:53911 original size:36 final size:36
Alignment explanation
Indices: 53851--54024 Score: 172
Period size: 36 Copynumber: 4.7 Consensus size: 36
53841 CATTTTTGAA
* * *
53851 AATATATAATATT-AAAACATTTTGAAAACTTATAT
1 AATATATAGTTTTAAAAACATTTTGAAAAATTATAT
* * *
53886 AATATATAGTTTTGAAATCATTTTGAAAAAATATAT
1 AATATATAGTTTTAAAAACATTTTGAAAAATTATAT
* *
53922 AATATATAGTTTCTTTAAAACCTTTTGAAAACACTTATAT
1 AATATATAG-TT-TTAAAAACATTTTGAAAA-A-TTATAT
*
53962 AAAATATAGTTTTAAAAAACACATTTTAGAAAAATTATAT
1 AATATATAGTTTT--AAAA-ACATTTT-GAAAAATTATAT
*
54002 AATATATAG-TTTAAAATCATTTT
1 AATATATAGTTTTAAAAACATTTT
54025 TTTTAAACTG
Statistics
Matches: 116, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
35 11 0.09
36 34 0.29
37 6 0.05
38 17 0.15
39 6 0.05
40 30 0.26
41 7 0.06
42 5 0.04
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (36 bp):
AATATATAGTTTTAAAAACATTTTGAAAAATTATAT
Found at i:53969 original size:40 final size:37
Alignment explanation
Indices: 53862--54013 Score: 171
Period size: 40 Copynumber: 4.0 Consensus size: 37
53852 ATATATAATA
*
53862 TTAAAACATTTTGAAAACTTATATAATATATAG-TTT
1 TTAAAACATTTTGAAAAATTATATAATATATAGTTTT
* * *
53898 TGAAATCATTTTGAAAAAATATATAATATATAGTTTCT
1 TTAAAACATTTTGAAAAATTATATAATATATAGTTT-T
* *
53936 TTAAAACCTTTTGAAAACACTTATATAAAATATAGTTTT
1 TTAAAACATTTTGAAAA-A-TTATATAATATATAGTTTT
**
53975 AAAAAACACATTTTAGAAAAATTATATAATATATAGTTT
1 -TTAAA-ACATTTT-GAAAAATTATATAATATATAGTTT
54014 AAAATCATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
36 29 0.30
37 2 0.02
38 15 0.16
39 2 0.02
40 36 0.38
41 7 0.07
42 5 0.05
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (37 bp):
TTAAAACATTTTGAAAAATTATATAATATATAGTTTT
Found at i:54076 original size:37 final size:36
Alignment explanation
Indices: 54035--54111 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
54025 TTTTAAACTG
** *
54035 ATATAAT-GTTTTTAAATCATTTTTTTAAAAAACTATA
1 ATATAATAGTTTGGAAATC-TTGTTTTAAAAAA-TATA
54072 ATAT-ATAGTTTGGAAATCTTGTTTTAAAAAATATA
1 ATATAATAGTTTGGAAATCTTGTTTTAAAAAATATA
54107 ATATA
1 ATATA
54112 TGGTTTAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 8 0.23
36 14 0.40
37 13 0.37
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATAATAGTTTGGAAATCTTGTTTTAAAAAATATA
Found at i:54108 original size:35 final size:37
Alignment explanation
Indices: 53999--54117 Score: 110
Period size: 35 Copynumber: 3.4 Consensus size: 37
53989 AGAAAAATTA
* **
53999 TATAATATATAGTTT-AAAATCATT-TTTT-TTAAAC
1 TATAATATATAGTTTGGAAATCATTGTTTTAAAAAAC
** *
54033 TGAT-ATA-AT-GTTTTTAAATCATTTTTTTAAAAAAC
1 T-ATAATATATAGTTTGGAAATCATTGTTTTAAAAAAC
54068 TATAATATATAGTTTGGAAATC-TTGTTTTAAAAAA-
1 TATAATATATAGTTTGGAAATCATTGTTTTAAAAAAC
*
54103 TATAATATATGGTTT
1 TATAATATATAGTTT
54118 AAAGATGTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
32 4 0.06
33 10 0.14
34 10 0.14
35 24 0.34
36 14 0.20
37 9 0.13
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (37 bp):
TATAATATATAGTTTGGAAATCATTGTTTTAAAAAAC
Found at i:54166 original size:3 final size:3
Alignment explanation
Indices: 54149--54194 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
54139 ATTATATAGT
*
54149 TTA TTA GTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA GTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
54193 TT
1 TT
54195 CGTTTTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:54212 original size:12 final size:11
Alignment explanation
Indices: 54163--54223 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
54153 TAGTATATTA
*
54163 TTATTATTATT
1 TTATTATTCTT
*
54174 ATTATTATTATT
1 -TTATTATTCTT
54186 TTAGTTATTCGTT
1 TTA-TTATTC-TT
54199 TTATTAATTCTTT
1 TTATT-ATTC-TT
54212 TTATT-TTCTT
1 TTATTATTCTT
54222 TT
1 TT
54224 TTTCTCGGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 4 0.09
11 6 0.14
12 18 0.41
13 16 0.36
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.70
Consensus pattern (11 bp):
TTATTATTCTT
Found at i:54764 original size:21 final size:20
Alignment explanation
Indices: 54740--54782 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
54730 CAGAACGAAA
54740 AAACCACAACACAAAAGAAGC
1 AAACCACAACACAAAA-AAGC
*
54761 AAACCACAACACCAAAAAGC
1 AAACCACAACACAAAAAAGC
54781 AA
1 AA
54783 GATATACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.63, C:0.30, G:0.07, T:0.00
Consensus pattern (20 bp):
AAACCACAACACAAAAAAGC
Found at i:55659 original size:11 final size:12
Alignment explanation
Indices: 55643--55671 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
55633 TCGAATAGAA
55643 TAATTTAAATT-
1 TAATTTAAATTC
55654 TAATTTAAATTC
1 TAATTTAAATTC
55666 TAATTT
1 TAATTT
55672 TGCAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATTTAAATTC
Found at i:56516 original size:19 final size:19
Alignment explanation
Indices: 56492--56529 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56482 TCGCATCATT
56492 TAAAAGAGGTGTTGATCCA
1 TAAAAGAGGTGTTGATCCA
56511 TAAAAGAGGTGTTGATCCA
1 TAAAAGAGGTGTTGATCCA
56530 CCAAAAACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (19 bp):
TAAAAGAGGTGTTGATCCA
Found at i:56541 original size:19 final size:19
Alignment explanation
Indices: 56493--56542 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
56483 CGCATCATTT
* *
56493 AAAAGAGGTGTTGATCCAT
1 AAAAGACGTGTTGATCCAC
*
56512 AAAAGAGGTGTTGATCCACC
1 AAAAGACGTGTTGATCCA-C
56532 AAAA-ACGTGTT
1 AAAAGACGTGTT
56543 TGTTAAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (19 bp):
AAAAGACGTGTTGATCCAC
Found at i:59154 original size:42 final size:41
Alignment explanation
Indices: 59095--59179 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 41
59085 GTCAACAAAC
59095 AACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCG
1 AACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACA-CG
*
59137 AACTTTTTAGTTTCATTCAGAGTCAATTTCAACTTCACACG
1 AACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACACG
59178 AA
1 AA
59180 GGATATTGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (41 bp):
AACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACACG
Found at i:59489 original size:110 final size:110
Alignment explanation
Indices: 59137--59512 Score: 618
Period size: 109 Copynumber: 3.5 Consensus size: 110
59127 CTTCACAGCG
* *
59137 AACTTTTTAGTTTCATTCAGAGTCAATTTCAACTTCACA-CGAAGGATATTGGACTCGAGACAAC
1 AACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
59201 ACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAAT
66 ACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAAT
* * * * *
59246 AACTTTTCAGTTTCATTCAGAGTCAATTTCAATTTCACATCAAAAGATATTGGACTC-AGAC-AC
1 AACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
59309 AC-AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAA-
66 ACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAAT
* *
59352 CACTTTTCAATTTCATACAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
1 AACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
* *
59417 ACAAGCTCAACTTCACAGCGAAGAGGCGATTGACTGTCAACAAAT
66 ACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAAT
59462 AACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT
1 AACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT
59513 AGCCTCAAAA
Statistics
Matches: 247, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
106 50 0.20
107 45 0.18
108 8 0.03
109 80 0.32
110 64 0.26
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (110 bp):
AACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
ACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAAT
Found at i:59826 original size:84 final size:84
Alignment explanation
Indices: 59676--60171 Score: 457
Period size: 84 Copynumber: 6.0 Consensus size: 84
59666 TCAGCTCCAA
* * * * * * * *
59676 GGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCGAAGACCCTCGAGTT
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTG-TAACCAAAGACCTTCGAGTT
59741 CGATTACACTCAGCTTCGAG
65 CGATTACACTCAGCTTCGAG
* * *
59761 GGCACATCATTTACAGCATAACTCAAGGCTAGAAAGATTATATGTGACCAAAGACCTTCGAGTTC
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTAACCAAAGACCTTCGAGTTC
59826 GATTACACTCAGCTTCGAG
66 GATTACACTCAGCTTCGAG
* * **
59845 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAAACAAAGACCTGGGAGTT-
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTAACCAAAGACCTTCGAGTTC
* * * *
59909 --TGACGCTCAGC-TCCAA
66 GATTACACTCAGCTTCGAG
* * * * * * * * *
59925 GGTACATCATTTGCA-CATAGCTTAAGTCTA-AAGGGCTATCTG---CCAAGGACCCTCGAGTTC
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTAACCAAAGACCTTCGAGTTC
*
59985 GATTACACTCAGCTTTGAG
66 GATTACACTCAGCTTCGAG
*
60004 GGCACATCATTTACAGCATAACTCAAGGCTAG-AAGGTTATCTGTCACC-AAGACCTTCGAGTTC
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTAACCAAAGACCTTCGAGTTC
* * * *
60067 AATTACGCTCAGC-TCCAA
66 GATTACACTCAGCTTCGAG
* * * * * * * *
60085 GGCACATCATTTGCAGCA-AAGCTTAAGTCGAGGAGGGCTATCTGCCAACCGAAA-ACCTTCGAG
1 GGCACATCATTTACAGCATAA-CTCAAGGCTAGAAAGGTTATCTG-TAACC-AAAGACCTTCGAG
*
60148 TTCGATTACATTCAGC-TC-AG
63 TTCGATTACACTCAGCTTCGAG
60168 GGCA
1 GGCA
60172 AACCAATATC
Statistics
Matches: 333, Mismatches: 64, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
75 12 0.04
78 20 0.06
79 27 0.08
80 39 0.12
81 36 0.11
82 33 0.10
83 10 0.03
84 117 0.35
85 39 0.12
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (84 bp):
GGCACATCATTTACAGCATAACTCAAGGCTAGAAAGGTTATCTGTAACCAAAGACCTTCGAGTTC
GATTACACTCAGCTTCGAG
Found at i:60757 original size:30 final size:32
Alignment explanation
Indices: 60721--60798 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 32
60711 TTAAAAAAAA
*
60721 TTGAAAATATAATATATGATTTTTAAA-CA-T
1 TTGAAAATATAATATATGATTTTGAAATCATT
*
60751 TTGAAAACT-TATATATATGGTTTTGAAATCATT
1 TTGAAAA-TATA-ATATATGATTTTGAAATCATT
60784 TTGAAAA-A-AATATAT
1 TTGAAAATATAATATAT
60799 ATATAGTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
30 15 0.37
31 16 0.39
32 2 0.05
33 8 0.20
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (32 bp):
TTGAAAATATAATATATGATTTTGAAATCATT
Found at i:60798 original size:34 final size:33
Alignment explanation
Indices: 60724--60835 Score: 104
Period size: 34 Copynumber: 3.4 Consensus size: 33
60714 AAAAAAATTG
*
60724 AAAATATAATATATGATTTTTAAACA-TTTG-AA
1 AAAATAT-ATATATGGTTTTTAAACATTTTGAAA
** *
60756 AACTTATATATATGGTTTTGAAATCATTTTGAAA
1 AAAATATATATATGGTTTTTAAA-CATTTTGAAA
* *
60790 AAAATATATATATAGTTCTTTAAAACCTTTTGAAA
1 AAAATATATATATGGTT-TTT-AAACATTTTGAAA
*
60825 AAACT-TATATA
1 AAAATATATATA
60836 AAAGTTTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
31 14 0.22
32 7 0.11
33 4 0.06
34 22 0.34
35 15 0.23
36 3 0.05
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (33 bp):
AAAATATATATATGGTTTTTAAACATTTTGAAA
Found at i:60827 original size:36 final size:34
Alignment explanation
Indices: 60658--60863 Score: 95
Period size: 34 Copynumber: 6.0 Consensus size: 34
60648 TTTAACATAC
* * *
60658 ATATGATATATAGTTTTGAAAACGGTTTTTTGAAATAT
1 ATAT-ATATATAGTTTTGAAAAC---ATTTTGAAAAAA
* * ** *
60696 ATATAGTATATAATTTT-AAAAAAAATTG-AAAAT
1 ATATA-TATATAGTTTTGAAAACATTTTGAAAAAA
* *
60729 ATA-ATATAT-GATTTT-TAAACA-TTTG-AAAAC
1 ATATATATATAG-TTTTGAAAACATTTTGAAAAAA
* * *
60759 TTATATATATGGTTTTGAAATCATTTTGAAAAAA
1 ATATATATATAGTTTTGAAAACATTTTGAAAAAA
* *
60793 ATATATATATAGTTCTTTAAAACCTTTTGAAAAAA
1 ATATATATATAGTT-TTGAAAACATTTTGAAAAAA
* * *
60828 CT-TATATAAAAGTTTTAAAAAAACATTTTTGAAAAA
1 ATATATAT-ATAGTTTT--GAAAACA-TTTTGAAAAA
60864 TTAATAATAT
Statistics
Matches: 132, Mismatches: 24, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
30 9 0.07
31 23 0.17
32 6 0.05
33 11 0.08
34 26 0.20
35 23 0.17
36 5 0.04
37 15 0.11
38 14 0.11
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (34 bp):
ATATATATATAGTTTTGAAAACATTTTGAAAAAA
Found at i:60888 original size:32 final size:32
Alignment explanation
Indices: 60851--60939 Score: 92
Period size: 34 Copynumber: 2.8 Consensus size: 32
60841 TTTAAAAAAA
*
60851 CATTTTTGAAAAATTAATAATATAATTTAAAT
1 CATTTTTTAAAAATTAATAATATAATTTAAAT
* * *
60883 CATTTTTTAAAAACTGATATAATGT-TTTTAAAT
1 CATTTTTTAAAAA-TTA-ATAATATAATTTAAAT
*
60916 CATTTTTTTAAAAACT-ATAATATA
1 CA-TTTTTTAAAAATTAATAATATA
60940 TAGTTTGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
31 6 0.13
32 12 0.26
33 11 0.24
34 17 0.37
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (32 bp):
CATTTTTTAAAAATTAATAATATAATTTAAAT
Found at i:61445 original size:18 final size:19
Alignment explanation
Indices: 61422--61460 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
61412 AGAACGAAAA
*
61422 AACCACAACA-CAAGAAGC
1 AACCACAACACCAAAAAGC
*
61440 AACCACGACACCAAAAAGC
1 AACCACAACACCAAAAAGC
61459 AA
1 AA
61461 GATATGCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.33, G:0.10, T:0.00
Consensus pattern (19 bp):
AACCACAACACCAAAAAGC
Found at i:61541 original size:64 final size:67
Alignment explanation
Indices: 61473--61604 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 67
61463 TATGCAACAA
61473 GCATTAAACCAAAAAAACAGAA-TGAAAAAGAAAGCA-TTTTTATCGGAGTCGAGAGG-GATCGT
1 GCATTAAACCAAAAAAACAGAACTGAAAAAGAAAGCATTTTTTATCGGAGTCGAGAGGAGATCGT
61535 CG
66 CG
61537 GCATTAAACCAAAAAAACAGAACTGAAAAAGAAAGCATTTTTTATCGGAGTCGAGAGGAGATCGT
1 GCATTAAACCAAAAAAACAGAACTGAAAAAGAAAGCATTTTTTATCGGAGTCGAGAGGAGATCGT
61602 CG
66 CG
61604 G
1 G
61605 GAGGGAAACG
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
64 22 0.34
65 14 0.22
66 20 0.31
67 9 0.14
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.19
Consensus pattern (67 bp):
GCATTAAACCAAAAAAACAGAACTGAAAAAGAAAGCATTTTTTATCGGAGTCGAGAGGAGATCGT
CG
Found at i:63136 original size:23 final size:22
Alignment explanation
Indices: 63110--63152 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
63100 CTCAACGTAA
63110 AATTATAAATTAATTACAAATCT
1 AATTATAAATTAATTA-AAATCT
* *
63133 AATTGTAAATTATTTAAAAT
1 AATTATAAATTAATTAAAAT
63153 AAAATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
AATTATAAATTAATTAAAATCT
Found at i:69728 original size:21 final size:22
Alignment explanation
Indices: 69702--69749 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
69692 ATTCTATACA
*
69702 TGAAAAGATTAAGTCATTTC-T
1 TGAAAAGATTAAGTCACTTCAT
*
69723 TGAAAAGGTTAAGTCACTTCAT
1 TGAAAAGATTAAGTCACTTCAT
69745 TGAAA
1 TGAAA
69750 TATAAGTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (22 bp):
TGAAAAGATTAAGTCACTTCAT
Found at i:72729 original size:12 final size:12
Alignment explanation
Indices: 72712--72737 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
72702 TGAAGTGCTT
72712 AGAGAGTGGAGA
1 AGAGAGTGGAGA
72724 AGAGAGTGGAGA
1 AGAGAGTGGAGA
72736 AG
1 AG
72738 TTTGATGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.08
Consensus pattern (12 bp):
AGAGAGTGGAGA
Found at i:76141 original size:17 final size:17
Alignment explanation
Indices: 76117--76164 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
76107 TAGATTTTAA
76117 AAGAAAATCCAACATTC
1 AAGAAAATCCAACATTC
* *
76134 AGGAAAATACATCACATTC
1 AAGAAAATCCA--ACATTC
*
76153 AAGAAGATCCAA
1 AAGAAAATCCAA
76165 ACTAAGGCAC
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (17 bp):
AAGAAAATCCAACATTC
Found at i:82719 original size:23 final size:23
Alignment explanation
Indices: 82693--82740 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
82683 ATAAAGTACA
*
82693 ATAACATACTAGGTAGCCCTTAT
1 ATAACATAATAGGTAGCCCTTAT
** *
82716 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCCCTTAT
82739 AT
1 AT
82741 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCCCTTAT
Found at i:82985 original size:30 final size:29
Alignment explanation
Indices: 82945--83011 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
82935 TCATTTGCAC
* * *
82945 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
82975 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
83004 AATAATAT
1 AA-AATAT
83012 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:83219 original size:23 final size:22
Alignment explanation
Indices: 83157--83228 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
83147 ACACTTTACA
*
83157 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
83180 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
83202 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
83225 ATAT
1 ATAT
83229 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.45
23 24 0.55
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:83689 original size:34 final size:34
Alignment explanation
Indices: 83649--83714 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
83639 AAGTTGTAGA
*
83649 TTTTGATTTCCTTTTGCTTGGCATCATATGAGAT
1 TTTTGATTTCCTTTTGCTTGGCACCATATGAGAT
83683 TTTTGATTTCCTTTTGCTTGGCACCATATGAG
1 TTTTGATTTCCTTTTGCTTGGCACCATATGAG
83715 CTTTGGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (34 bp):
TTTTGATTTCCTTTTGCTTGGCACCATATGAGAT
Found at i:84009 original size:18 final size:18
Alignment explanation
Indices: 83986--84022 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
83976 CGAAATATAT
83986 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
84004 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAACTCAA
84022 A
1 A
84023 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:84491 original size:21 final size:21
Alignment explanation
Indices: 84433--84493 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
84423 AAAAAGGATA
84433 GATACT-TTACA--ATATAAC
1 GATACTATTACATTATATAAC
*
84451 CACTACCTATTACATTATATAAC
1 GA-TA-CTATTACATTATATAAC
84474 GATACTATTACATTATATAA
1 GATACTATTACATTATATAA
84494 GCGCAACCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 2 0.06
21 21 0.58
22 2 0.06
23 8 0.22
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (21 bp):
GATACTATTACATTATATAAC
Found at i:84493 original size:44 final size:41
Alignment explanation
Indices: 84433--84514 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
84423 AAAAAGGATA
* *
84433 GATACTTTACAATATAACCACTACCTATTACATTATATAAC
1 GATACTTTACAATATAACCACAACCTATTACATCATATAAC
* *
84474 GATACTATTACATTATATAAGCGCAACCTATTACATCATAT
1 GATACT-TTACA--ATATAACCACAACCTATTACATCATAT
84515 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 6 0.18
42 5 0.15
44 23 0.68
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (41 bp):
GATACTTTACAATATAACCACAACCTATTACATCATATAAC
Found at i:84504 original size:23 final size:22
Alignment explanation
Indices: 84444--84514 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
84434 ATACTTTACA
*
84444 ATATAACCACTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
84467 ATATAACGATA-CTATTACATT
1 ATATAACGATACCTATTACATT
*
84488 ATATAAGCGCA-ACCTATTACATC
1 ATATAA-CG-ATACCTATTACATT
84511 ATAT
1 ATAT
84515 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 16 0.37
22 5 0.12
23 22 0.51
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:84555 original size:21 final size:22
Alignment explanation
Indices: 84530--84579 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
84520 CCTATTATAT
84530 TAAAAGTG-TCCATACTTTTTA
1 TAAAAGTGATCCATACTTTTTA
* *
84551 TAAAAAG-GATCGATACTTTTTT
1 T-AAAAGTGATCCATACTTTTTA
84573 TAAAAGT
1 TAAAAGT
84580 TATGTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (22 bp):
TAAAAGTGATCCATACTTTTTA
Found at i:84908 original size:25 final size:25
Alignment explanation
Indices: 84851--84916 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
84841 CACTCAAAAG
*
84851 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
84876 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
84901 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
84917 TAATGATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:87391 original size:3 final size:3
Alignment explanation
Indices: 87383--87463 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
87373 ACTTGTTTGG
* * **
87383 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
87431 AAC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
87464 GTCAGCTTCA
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:87400 original size:12 final size:12
Alignment explanation
Indices: 87387--87475 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
87377 GTTTGGATCA
* *
87387 TCATCTTCATCA
1 TCATCGTCATCT
* *
87399 TCATCATCATCA
1 TCATCGTCATCT
*
87411 TCATCATCATCT
1 TCATCGTCATCT
* *
87423 TCATCGCCAACT
1 TCATCGTCATCT
*
87435 TCATCGTCATCA
1 TCATCGTCATCT
87447 TCATCGTCATCT
1 TCATCGTCATCT
*
87459 TCATCGTCAGCT
1 TCATCGTCATCT
87471 TCATC
1 TCATC
87476 TTCTGCGACC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:87406 original size:18 final size:18
Alignment explanation
Indices: 87387--87478 Score: 85
Period size: 18 Copynumber: 5.1 Consensus size: 18
87377 GTTTGGATCA
* *
87387 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
87405 TCATCATCATCATCATCT
1 TCATCATCATCATCATCT
** * * *
87423 TCATCGCCAACTTCATCG
1 TCATCATCATCATCATCT
*
87441 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
87459 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
87477 TC
1 TC
87479 TGCGACCGCT
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.05, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:87439 original size:36 final size:36
Alignment explanation
Indices: 87399--87475 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
87389 ATCTTCATCA
87399 TCATCATCATCATCATCATCATCTTCATCGCCAACT
1 TCATCATCATCATCATCATCATCTTCATCGCCAACT
* * * *
87435 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAACT
87471 TCATC
1 TCATC
87476 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAACT
Found at i:87478 original size:6 final size:6
Alignment explanation
Indices: 87387--87478 Score: 76
Period size: 6 Copynumber: 15.3 Consensus size: 6
87377 GTTTGGATCA
* * * * * * *
87387 TCATCT TCATCA TCATCA TCATCA TCATCA TCATCT TCATCG CCAACT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
87435 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
87479 TGCGACCGCT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.23, C:0.35, G:0.05, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:89270 original size:194 final size:195
Alignment explanation
Indices: 88924--89879 Score: 1583
Period size: 198 Copynumber: 4.9 Consensus size: 195
88914 TTTAAATTAG
88924 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAAC---ATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
88989 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
63 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
89054 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
128 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
89119 AAA
193 AAA
*
89122 TATCGACACAAAC-TTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTGTAATT
1 TATCGACACAAACATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATT
89186 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGA
66 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGA
89251 CACTTTTTATATATGGATCGACACTTTATGGGT-----CTGTTTTCCATTCATTCTGG-AAAAAA
131 CACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAA
**
89310 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACATGTATA
1 TATCGACACAAAC---ATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
89375 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
63 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
89440 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
128 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
89505 AAA
193 AAA
89508 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAAC---ATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
89573 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
63 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
89636 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTAGAAAA
128 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
89701 GAAA
193 -AAA
* * * * * *
89705 CATCGATACAAACTATATTAGTGTCGACACATTATTTAGACATATTTTTTCATAAAACCGGTAGA
1 TATCGACACAAAC---ATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
* * *
89770 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
63 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
89835 TTGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
127 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
89880 GGCCATATTG
Statistics
Matches: 727, Mismatches: 17, Indels: 28
0.94 0.02 0.04
Matches are distributed among these distances:
188 19 0.03
189 20 0.03
192 146 0.20
194 148 0.20
196 87 0.12
197 121 0.17
198 156 0.21
199 9 0.01
200 21 0.03
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (195 bp):
TATCGACACAAACATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATT
GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGA
CACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAA
Found at i:90017 original size:19 final size:19
Alignment explanation
Indices: 89993--90037 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
89983 TTATATTCAC
89993 ATACAAAAATATAAATCGT
1 ATACAAAAATATAAATCGT
* *
90012 ATACAAAATTATAAATCTT
1 ATACAAAAATATAAATCGT
90031 ATACAAA
1 ATACAAA
90038 TTAACCCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (19 bp):
ATACAAAAATATAAATCGT
Found at i:91854 original size:33 final size:33
Alignment explanation
Indices: 91817--91882 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
91807 CATCTTAATA
*
91817 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
91850 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
91883 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:91941 original size:21 final size:21
Alignment explanation
Indices: 91916--91980 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
91906 CCCCTTATGC
* *
91916 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
91937 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
91958 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
91979 CT
1 CT
91981 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:94226 original size:17 final size:18
Alignment explanation
Indices: 94204--94246 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
94194 ATATATCCGG
94204 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
94221 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
94241 TATCAT
1 TATCAT
94247 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:94255 original size:20 final size:19
Alignment explanation
Indices: 94209--94255 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
94199 TCCGGTATCA
94209 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
94228 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
94249 TTTTACC
1 TTTTACC
94256 TGTATCGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:94431 original size:20 final size:19
Alignment explanation
Indices: 94386--94431 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
94376 TCCGGTAACG
94386 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
94405 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
94426 TTTTAC
1 TTTTAC
94432 TTGGTATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:94597 original size:182 final size:180
Alignment explanation
Indices: 94176--94644 Score: 667
Period size: 182 Copynumber: 2.6 Consensus size: 180
94166 CGTACTTACG
* *
94176 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
94241 TATCATATTTTTACCT-G--TATCGTTGTGGATCGATATTTTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATAATTTTTTAAAAGTATCGACACATTATA
* *
94303 GGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
94353 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
94418 TATCATATTTTTACTTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATA-ATTTTTTAAAAGTATCGACACATTAT
** *
94483 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * *
94535 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * * *
94599 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACATATTTTT
65 TTATCATATTTTTACCTGGTATATCGTTTTGGATCGATA-ATTTTT
94645 AATTTGGATC
Statistics
Matches: 259, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
177 76 0.29
178 1 0.00
180 17 0.07
181 68 0.26
182 96 0.37
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGGTATATCGTTTTGGATCGATAATTTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:95278 original size:223 final size:225
Alignment explanation
Indices: 94711--95414 Score: 1229
Period size: 223 Copynumber: 3.1 Consensus size: 225
94701 ACCTACTTTT
*
94711 ATAAGTATGGACACTTTTATAAAAATGATATATTTTTTTAAAGTTATGTAATTTATGTTTCAATT
1 ATAAGTATGGACACTTTTATAAAAATGATATATTTTTTGAAAGTTATGTAATTTATGTTTCAATT
* * *
94776 TATTTAATAGTGTTTCATGTTTTCCACCTAC-ATATTAATTTAATAATTTAATTTACACAAAATA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
94840 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
131 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
*
94905 ATATAATAATAAATATG-TTTCAACAGTGAA
196 AGATAATAAT-AATATGTTTTCAACAGTGAA
94935 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTGAAAGTTATGTAATTTATGTTTCAA
1 ATAAGTATGGACACTTTTATAAAAATGATATAT--TTTTTGAAAGTTATGTAATTTATGTTTCAA
95000 TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAA
64 TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAA
*
95065 AATTATTTGATAGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACC
129 AATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACC
95130 AAA-ATAATAAT-ATATGTTTTCAACAGTGAA
194 AAAGATAATAATAATATGTTTTCAACAGTGAA
*
95160 ATAAGTATGGACACTTTTATAAAAAAGATATATTTTTTGAAAGTTATGTAATTTATGTTTCAATT
1 ATAAGTATGGACACTTTTATAAAAATGATATATTTTTTGAAAGTTATGTAATTTATGTTTCAATT
*
95225 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTATACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
* *
95290 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAACTAA
131 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
*
95355 AGATAATAATAAATATATTTTC-ACAGTGAA
196 AGATAATAAT-AATATGTTTTCAACAGTGAA
*
95385 ATAAGTATGGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
95415 GATAATTTAC
Statistics
Matches: 461, Mismatches: 12, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
223 159 0.34
224 46 0.10
225 82 0.18
226 78 0.17
227 96 0.21
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (225 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATTTTTTGAAAGTTATGTAATTTATGTTTCAATT
TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
AGATAATAATAATATGTTTTCAACAGTGAA
Found at i:106498 original size:234 final size:234
Alignment explanation
Indices: 106089--106555 Score: 864
Period size: 234 Copynumber: 2.0 Consensus size: 234
106079 TGGCTCTGAT
106089 ACCAATTGTTGCGGAATACGACTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGAAAATAA
1 ACCAATTGTTGCGGAATACGACTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGAAAATAA
106154 AAATGAAGATAAAGAAGACACAAATTTTACGTGGAAAACCCCTAAATAATATAAGGTAAAAAACC
66 AAATGAAGATAAAGAAGACACAAATTTTACGTGGAAAACCCCTAAATAATATAAGGTAAAAAACC
* *
106219 ACGGGTAAATGTAGAAAAAATTCACTATGAGAAAATATGAATTACAACTTCTCTCGATCTTACAA
131 ACGGGCAAATGTAGAAAAAATTCACTATGAGAAAATATGAATTACAACTTCTCTCGATCTAACAA
*
106284 GGAGAAACAATGACGATTCTCTCTTAATAAAAAGGAGAC
196 GGAGAAACAATGACAATTCTCTCTTAATAAAAAGGAGAC
*
106323 ACCAATTGTTGCGGAATACGACTATCGGATAGAGCAAAATCGCAACTGATATTTTG-GAAAAATA
1 ACCAATTGTTGCGGAATACGACTATCGGATAGAGCAAAATCGCAACTGATAATTTGAG-AAAATA
**
106387 AAAATGAAGATAAAGAAGACACAAATTTTACGTGGAAAACCCCTAAATAATATCGGGTAAAAAAC
65 AAAATGAAGATAAAGAAGACACAAATTTTACGTGGAAAACCCCTAAATAATATAAGGTAAAAAAC
106452 CACGGGCAAATGTAGAAAAAATTCACTATGAGAAAATATGAATTACAACTTCTCTCGATCTAACA
130 CACGGGCAAATGTAGAAAAAATTCACTATGAGAAAATATGAATTACAACTTCTCTCGATCTAACA
106517 AGGAGAAACAATGACAATTCTCTCTTAATAAAAAGGAGA
195 AGGAGAAACAATGACAATTCTCTCTTAATAAAAAGGAGA
106556 AAACAACTCT
Statistics
Matches: 226, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
233 1 0.00
234 225 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (234 bp):
ACCAATTGTTGCGGAATACGACTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGAAAATAA
AAATGAAGATAAAGAAGACACAAATTTTACGTGGAAAACCCCTAAATAATATAAGGTAAAAAACC
ACGGGCAAATGTAGAAAAAATTCACTATGAGAAAATATGAATTACAACTTCTCTCGATCTAACAA
GGAGAAACAATGACAATTCTCTCTTAATAAAAAGGAGAC
Found at i:119542 original size:17 final size:18
Alignment explanation
Indices: 119516--119549 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
119506 AACTCAACTG
*
119516 AAAATCTATT-AATTTGA
1 AAAATATATTAAATTTGA
119533 AAAATATATTAAATTTG
1 AAAATATATTAAATTTG
119550 GTTAAATAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (18 bp):
AAAATATATTAAATTTGA
Found at i:133917 original size:21 final size:21
Alignment explanation
Indices: 133891--133954 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
133881 ATAATCTCTT
133891 GCATGTCTGAACCTACAACAA
1 GCATGTCTGAACCTACAACAA
133912 GCATGTCTGAACCTACAACAA
1 GCATGTCTGAACCTACAACAA
* *
133933 GCATGTCATCAACATACAACAA
1 GCATGTC-TGAACCTACAACAA
133955 TAACATAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 28 0.70
22 12 0.30
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (21 bp):
GCATGTCTGAACCTACAACAA
Found at i:136350 original size:64 final size:63
Alignment explanation
Indices: 136277--136396 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
136267 ATTGTTCAAG
** * *
136277 GTGTATCGATGCACGTGAAGTGCATCGATACACTACTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATACACCACCTT-AAATAAAAACATCGAATGCCATCA
* * * *
136341 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCGATACACCACCTTAAATAAAAACATCGAAT
136397 AGGATTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 16 0.33
64 32 0.67
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATACACCACCTTAAATAAAAACATCGAATGCCATCA
Found at i:137150 original size:23 final size:23
Alignment explanation
Indices: 137082--137142 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
137072 CAATCTTATA
*
137082 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
137105 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
137128 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
137143 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:143347 original size:64 final size:64
Alignment explanation
Indices: 143242--143403 Score: 170
Period size: 63 Copynumber: 2.5 Consensus size: 64
143232 CCAGTTCAAG
** * * ** *
143242 GTGTATCGATGCACGTGAAGTGCATCGATACACTACTTTAAAATAAAAACATCGAAT-GCCA-TC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATAG-CATTC
143305 A
64 A
* * *
143306 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATAGGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATAGCATTCA
*
143370 -TGTATCGATGCA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
143404 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.02
63 47 0.56
64 35 0.42
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATAGCATTCA
Found at i:144076 original size:23 final size:23
Alignment explanation
Indices: 144044--144102 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
144034 ATCTTATATG
*
144044 GCACTACGGTGCAATTCTACGCGA
1 GCACTTCGGTGCAATTCTACG-GA
* *
144068 -CACTTCGGTGCAATTCTATGTA
1 GCACTTCGGTGCAATTCTACGGA
144090 GCACTTCGGTGCA
1 GCACTTCGGTGCA
144103 TTTATACGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGGA
Found at i:148482 original size:26 final size:26
Alignment explanation
Indices: 148453--148510 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
148443 GATATACTGA
148453 TAAATCGACATGAATCTTAAATACTC
1 TAAATCGACATGAATCTTAAATACTC
148479 TAAATCGACATGAATCTTAAATACTC
1 TAAATCGACATGAATCTTAAATACTC
148505 TAAATC
1 TAAATC
148511 ATCATTTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (26 bp):
TAAATCGACATGAATCTTAAATACTC
Found at i:151697 original size:29 final size:29
Alignment explanation
Indices: 151655--151713 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
151645 ATTTTCACCT
* *
151655 AACTAAATTGATGTAAGCAATGAAATCAA
1 AACTAAATTAATGTAAGAAATGAAATCAA
151684 AACTAAATTAATGTAAGAAATGAAATCAA
1 AACTAAATTAATGTAAGAAATGAAATCAA
151713 A
1 A
151714 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGAAATGAAATCAA
Found at i:158058 original size:29 final size:29
Alignment explanation
Indices: 158016--158074 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
158006 ATTTTCACTT
158016 AACTAAATTGATGTAA-ACAATGACATCAA
1 AACTAAATTGATGTAAGA-AATGACATCAA
*
158045 AACTAAATTGATGTAAGAAATGGCATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
158074 A
1 A
158075 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGAAATGACATCAA
Found at i:160445 original size:2 final size:2
Alignment explanation
Indices: 160438--160469 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
160428 TTAATATTAA
160438 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
160470 TGAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:170382 original size:29 final size:30
Alignment explanation
Indices: 170348--170432 Score: 118
Period size: 29 Copynumber: 2.8 Consensus size: 30
170338 ATATTATCTT
170348 AAGTAAGATTTTTCACCATAAACTCG-TTA
1 AAGTAAGATTTTTCACCATAAACTCGCTTA
*
170377 AAGTAAGATTTTTCACCATAAATTCGACCTTA
1 AAGTAAGATTTTTCACCATAAACTCG--CTTA
* *
170409 AAATAAGATTTTTCATCATAAACT
1 AAGTAAGATTTTTCACCATAAACT
170433 TACCATAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 25 0.51
32 24 0.49
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.35
Consensus pattern (30 bp):
AAGTAAGATTTTTCACCATAAACTCGCTTA
Found at i:170416 original size:32 final size:29
Alignment explanation
Indices: 170351--170432 Score: 110
Period size: 32 Copynumber: 2.7 Consensus size: 29
170341 TTATCTTAAG
*
170351 TAAGATTTTTCACCATAAACTCGTTAAAG
1 TAAGATTTTTCACCATAAACTCGTTAAAA
*
170380 TAAGATTTTTCACCATAAATTCGACCTTAAAA
1 TAAGATTTTTCACCATAAACTCG---TTAAAA
*
170412 TAAGATTTTTCATCATAAACT
1 TAAGATTTTTCACCATAAACT
170433 TACCATAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 22 0.48
32 24 0.52
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (29 bp):
TAAGATTTTTCACCATAAACTCGTTAAAA
Found at i:175176 original size:29 final size:29
Alignment explanation
Indices: 175127--175188 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
175117 AATAAAAGGA
* *
175127 ATTAAAAATATAGTAT-TAAAATGTAAAAT
1 ATTAAAAATATAATATCAAAAATG-AAAAT
175156 ATTAAAAATA-AATAGTCAAAAATGAAAAT
1 ATTAAAAATATAATA-TCAAAAATGAAAAT
175185 -TTAA
1 ATTAA
175189 TGATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 7 0.24
29 16 0.55
30 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTAAAAATATAATATCAAAAATGAAAAT
Found at i:176355 original size:3 final size:3
Alignment explanation
Indices: 176347--176406 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
176337 GGCCTGTTTG
* * *
176347 TAA TAA TAA AAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
176393 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
176407 TAAATAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:176367 original size:15 final size:15
Alignment explanation
Indices: 176347--176413 Score: 82
Period size: 15 Copynumber: 4.4 Consensus size: 15
176337 GGCCTGTTTG
176347 TAATAATAAAAATAT
1 TAATAATAAAAATAT
176362 TAATAATAAAAATAT
1 TAATAATAAAAATAT
*
176377 ATAATAAATAATAATA-
1 -TAAT-AATAAAAATAT
*
176393 TAATAATAATAATAT
1 TAATAATAAAAATAT
*
176408 AAATAA
1 TAATAA
176414 AATCGGGACA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
14 10 0.21
15 24 0.51
16 4 0.09
17 9 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATAAAAATAT
Found at i:176774 original size:114 final size:114
Alignment explanation
Indices: 176635--177081 Score: 643
Period size: 114 Copynumber: 3.9 Consensus size: 114
176625 TAGAGTCATG
** * * *
176635 CAAAAGGTT-GAACAAGCTCTTCTCATTATGAACTTCTTCTT-ATTGCTTCAGATGAGTTCTTCT
1 CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCCTT-CTTCAGATGAGTTCTTCT
*
176698 CATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
65 CATTATGAACTCTTC-CTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
*
176748 CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCTTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
*
176813 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
66 ATTATGAACTCTTC-CTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
* * * *
176862 CAAAAAGTTGGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTT
1 CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * *
176927 ATTATGAACTCGGCCTGGAAATA-CTGATCCATCAAGTGATGAATTCGAG
66 ATTATGAACTCTTCCTGGAAA-AGTTGATCCATCAAGTGATGAATTCAAA
176976 CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
177041 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATG
66 ATTATGAACTCTTCCTGGAAAAGTTGATCCATCAAGTGATG
177082 GAAATTTCTG
Statistics
Matches: 304, Mismatches: 25, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
113 9 0.03
114 291 0.96
115 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (114 bp):
CAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTCCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
Found at i:177124 original size:37 final size:36
Alignment explanation
Indices: 177083--177276 Score: 119
Period size: 37 Copynumber: 5.3 Consensus size: 36
177073 CAAGTGATGG
*
177083 AAATTTCTGTTTCGAATGAGACTGTCTCAAGCGAGAC
1 AAATTT-TGTTTCGAATGAAACTGTCTCAAGCGAGAC
* ** * *
177120 AAATTTTGTTT-TAA-GAAAAACAATCTCAAGTGAGAT
1 AAATTTTGTTTCGAATG--AAACTGTCTCAAGCGAGAC
* * *
177156 AAAGTTCTGTTTCGAGTGAAACTGTCTCGAGCGAGAC
1 AAA-TTTTGTTTCGAATGAAACTGTCTCAAGCGAGAC
* ** * *
177193 AAATTTTGTTT-TAA-GAAAAACAATCTCAAGTGAGAT
1 AAATTTTGTTTCGAATG--AAACTGTCTCAAGCGAGAC
* * * *
177229 AAAGTTCTGTTTC-AAGTGAAACTGTCTCGAGCAAGAT
1 AAA-TTTTGTTTCGAA-TGAAACTGTCTCAAGCGAGAC
177266 AAATTTTGTTT
1 AAATTTTGTTT
177277 TAAGAAAAAC
Statistics
Matches: 117, Mismatches: 29, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
34 2 0.02
35 3 0.03
36 53 0.45
37 56 0.48
38 1 0.01
39 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (36 bp):
AAATTTTGTTTCGAATGAAACTGTCTCAAGCGAGAC
Found at i:177147 original size:36 final size:36
Alignment explanation
Indices: 177107--177306 Score: 193
Period size: 36 Copynumber: 5.5 Consensus size: 36
177097 AATGAGACTG
*
177107 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGATAAATTTTGTTTTAAGAAAAACAA
* * ** ** **
177143 TCTCAAGTGAGATAAAGTTCTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGATAAA-TTTTGTTTTAAGAAAAACAA
* *
177180 TCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGATAAATTTTGTTTTAAGAAAAACAA
* * * ** **
177216 TCTCAAGTGAGATAAAGTTCTGTTTCAAGTGAAACTG
1 TCTCAAGCGAGATAAA-TTTTGTTTTAAGAAAAACAA
* *
177253 TCTCGAGCAAGATAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGATAAATTTTGTTTTAAGAAAAACAA
*
177289 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGATAAATT
177307 GCTATTTGAA
Statistics
Matches: 122, Mismatches: 40, Indels: 4
0.73 0.24 0.02
Matches are distributed among these distances:
36 69 0.57
37 53 0.43
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGATAAATTTTGTTTTAAGAAAAACAA
Found at i:177166 original size:73 final size:73
Alignment explanation
Indices: 177087--177304 Score: 375
Period size: 73 Copynumber: 3.0 Consensus size: 73
177077 TGATGGAAAT
* *
177087 TTCTGTTTCGAATGAGACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
1 TTCTGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
177152 AGATAAAG
66 AGATAAAG
*
177160 TTCTGTTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
1 TTCTGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
177225 AGATAAAG
66 AGATAAAG
* *
177233 TTCTGTTTC-AAGTGAAACTGTCTCGAGCAAGATAAATTTTGTTTTAAGAAAAACAATCTCAAGT
1 TTCTGTTTCGAA-TGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGT
177297 GAGATAAA
65 GAGATAAA
177305 TTGCTATTTG
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
72 1 0.01
73 137 0.99
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (73 bp):
TTCTGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
AGATAAAG
Found at i:178038 original size:22 final size:22
Alignment explanation
Indices: 178013--178092 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
178003 AATAAAGCTT
178013 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
*
178035 TCATCTTT-AAAGAGAGAGTATA
1 TCATCTTTGAAA-AGAGAATATA
* * **
178057 TCAGCTTTGAAGAGAGAACCTA
1 TCATCTTTGAAAAGAGAATATA
178079 TCATCTTTGAAAAG
1 TCATCTTTGAAAAG
178093 TGTAGATGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.06
22 43 0.90
23 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:182687 original size:21 final size:22
Alignment explanation
Indices: 182652--182696 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
182642 GTTACGAAAG
182652 AAAGGGATAAAAAGGCCCAAAT
1 AAAGGGATAAAAAGGCCCAAAT
182674 AAAGGGAT-AAAAGGCCCAAAT
1 AAAGGGATAAAAAGGCCCAAAT
182695 AA
1 AA
182697 GTGTTTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.56, C:0.13, G:0.22, T:0.09
Consensus pattern (22 bp):
AAAGGGATAAAAAGGCCCAAAT
Found at i:183006 original size:31 final size:27
Alignment explanation
Indices: 182925--183008 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 27
182915 CTTGATTCAA
*
182925 TTTTCCTTTTTCTTCTTC-TTCTTTTT
1 TTTTCTTTTTTCTTCTTCTTTCTTTTT
*
182951 TTGTTCTCTTTTTCTTTTTCTTTCTTTTCCAT
1 TT-TTCT-TTTTTCTTCTTCTTTCTTTT---T
182983 TTTTCTTTTTTCCTTCTTCTTTCTTT
1 TTTTCTTTTTT-CTTCTTCTTTCTTT
183009 GCTGGATGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 11 0.23
29 7 0.15
30 5 0.10
31 17 0.35
32 3 0.06
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.75
Consensus pattern (27 bp):
TTTTCTTTTTTCTTCTTCTTTCTTTTT
Found at i:183305 original size:2 final size:2
Alignment explanation
Indices: 183298--183338 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
183288 ACAAAGGATA
*
183298 AT AT AT AT AT AT AT AT AT AT TT AT -T 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
183339 TAAAGGATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:183327 original size:17 final size:17
Alignment explanation
Indices: 183298--183340 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
183288 ACAAAGGATA
183298 ATATATA-TATATATAT
1 ATATATATTATATATAT
*
183314 ATATTTATTATATATAT
1 ATATATATTATATATAT
183331 ATATATATTA
1 ATATATATTA
183341 AAGGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATATTATATATAT
Found at i:184764 original size:270 final size:271
Alignment explanation
Indices: 184273--184822 Score: 1052
Period size: 270 Copynumber: 2.0 Consensus size: 271
184263 GGGCATAAGG
184273 CTTTGGTGACACCTTCACCAATCTTGGTGTAATGTATTGACCTTTAACCAATGAGGGTACAGGTC
1 CTTTGG-GACACCTTCACCAATCTTGGTGTAATGTATTGACCTTTAACCAATGAGGGTACAGGTC
184338 TAAGATAGATTCTTGAAACACCTTCAGAGTTTTCTCGCTCGCGAGGCTATCACTTTCTTTGATCG
65 TAAGATAGATTCTTGAAACACCTTCAGAGTTTTCTCGCTCGCGAGGCTATCACTTTCTTTGATCG
184403 TTCTGAATGAATGAATGCTCTCATGTTATCGAGGGGGTTCTGAATGCTCATTCGGCTCTAACTGG
130 TTCTGAATGAATGAATGCTCTCATGTTATCGAGGGGGTTCTGAATGCTCATTCGGCTCTAACTGG
184468 GGTAATATTAACCAGATTTCTTAAGTTATCCTTTGCCTTACTGGTTTTCAAAAAATCTGATACTG
195 GGTAATATTAACCAGATTTCTTAAGTTATCCTTTGCCTTACTGGTTTTCAAAAAATCTGATACTG
184533 TATCTGAGGTGT
260 TATCTGAGGTGT
184545 CTTTGGGACACCTTCACCAATCTTGGTGTAATGTATTGACCTTTAACCAAATGAGGGTACAGGTC
1 CTTTGGGACACCTTCACCAATCTTGGTGTAATGTATTGACCTTTAACC-AATGAGGGTACAGGTC
184610 TAAGATAGATTCTTGAAACACCTTCAGAG-TTT-TCGCTCGCGAGGCTATCAC-TTCTTTGATCG
65 TAAGATAGATTCTTGAAACACCTTCAGAGTTTTCTCGCTCGCGAGGCTATCACTTTCTTTGATCG
184672 TTCTGAATGAATGAATGCTCTCATGTTATCGAGGGGGTTCTGAATGCTCATTTCGGCTCTAACTG
130 TTCTGAATGAATGAATGCTCTCATGTTATCGAGGGGGTTCTGAATGCTCA-TTCGGCTCTAACTG
184737 GGGTAATATTAACCAGATTTCTTAAGTTATCCTTTGCCTTACTGGTTTTCAAAAAATCTGATACT
194 GGGTAATATTAACCAGATTTCTTAAGTTATCCTTTGCCTTACTGGTTTTCAAAAAATCTGATACT
184802 GTATCTGAGGTGT
259 GTATCTGAGGTGT
184815 CTTTGGGA
1 CTTTGGGA
184823 GTTTCTGTTG
Statistics
Matches: 276, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
269 61 0.22
270 119 0.43
271 45 0.16
272 51 0.18
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (271 bp):
CTTTGGGACACCTTCACCAATCTTGGTGTAATGTATTGACCTTTAACCAATGAGGGTACAGGTCT
AAGATAGATTCTTGAAACACCTTCAGAGTTTTCTCGCTCGCGAGGCTATCACTTTCTTTGATCGT
TCTGAATGAATGAATGCTCTCATGTTATCGAGGGGGTTCTGAATGCTCATTCGGCTCTAACTGGG
GTAATATTAACCAGATTTCTTAAGTTATCCTTTGCCTTACTGGTTTTCAAAAAATCTGATACTGT
ATCTGAGGTGT
Found at i:186401 original size:14 final size:14
Alignment explanation
Indices: 186367--186420 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
186357 CATAAAAATA
* *
186367 CAAATGCAAAGATG
1 CAAATGTAAATATG
186381 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
186396 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
186410 TAAATGTAAAT
1 CAAATGTAAAT
186421 TATTTAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:187556 original size:29 final size:28
Alignment explanation
Indices: 187497--187555 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
187487 ATGAAACATT
*
187497 AATAATAATATACATATAAATATTATGAA
1 AATAATAATATA-ATATAAAAATTATGAA
*
187526 AATAATAAGTAT-ATATAAAAATTTTGAA
1 AATAATAA-TATAATATAAAAATTATGAA
187554 AA
1 AA
187556 AGAAGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 16 0.59
29 8 0.30
30 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (28 bp):
AATAATAATATAATATAAAAATTATGAA
Found at i:187963 original size:54 final size:54
Alignment explanation
Indices: 187882--187989 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
187872 ATTCGTGGTC
187882 GGTTACGTTAGGGAAGGATTAGCACCCCTACAAC-CCCAAAATTGGTAGTTTTT
1 GGTTACGTTAGGGAAGGATTAGCACCCCTACAACGCCCAAAATTGGTAGTTTTT
187935 GGTTACGTTTAGGGAAGGATTAGCACCCCTACAACGCCCAAAATTGGTAGTTTTT
1 GGTTACG-TTAGGGAAGGATTAGCACCCCTACAACGCCCAAAATTGGTAGTTTTT
187990 AATTATAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
53 7 0.13
54 27 0.51
55 19 0.36
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (54 bp):
GGTTACGTTAGGGAAGGATTAGCACCCCTACAACGCCCAAAATTGGTAGTTTTT
Found at i:188934 original size:27 final size:27
Alignment explanation
Indices: 188896--188958 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
188886 CTCATTTCTC
*
188896 TTCTCTCTCTTAAACTGAGAGAGAGAT
1 TTCTCTCTCTTAAACTGAGAGACAGAT
188923 TTCTCTCTCTTAAACTGAGAGACAGAT
1 TTCTCTCTCTTAAACTGAGAGACAGAT
188950 TTCTCTCTC
1 TTCTCTCTC
188959 GCCTCTCTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (27 bp):
TTCTCTCTCTTAAACTGAGAGACAGAT
Found at i:189346 original size:21 final size:21
Alignment explanation
Indices: 189316--189368 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
189306 GGTTGTATTA
189316 TGGTG-GTCACCAAACTATAG
1 TGGTGAGTCACCAAACTATAG
189336 TGGTGAGTCACCAAACTATAG
1 TGGTGAGTCACCAAACTATAG
*
189357 TGGTGACTCACC
1 TGGTGAGTCACC
189369 GTAGCCCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
TGGTGAGTCACCAAACTATAG
Found at i:191457 original size:13 final size:13
Alignment explanation
Indices: 191439--191464 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191429 TTGGGTACTG
191439 TGTAATTTCCAGT
1 TGTAATTTCCAGT
191452 TGTAATTTCCAGT
1 TGTAATTTCCAGT
191465 AAAACTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TGTAATTTCCAGT
Found at i:193277 original size:10 final size:10
Alignment explanation
Indices: 193245--193332 Score: 85
Period size: 10 Copynumber: 9.0 Consensus size: 10
193235 AGAAAACTGG
193245 TTTGACCGGT
1 TTTGACCGGT
*
193255 TTTGAACCTGT
1 TTTG-ACCGGT
193266 TTTGACCGG-
1 TTTGACCGGT
*
193275 TTTGACCTGT
1 TTTGACCGGT
193285 TTTGACCGG-
1 TTTGACCGGT
*
193294 TTTGATCGGT
1 TTTGACCGGT
*
193304 TTCGACCGG-
1 TTTGACCGGT
*
193313 TTCGAACCGG-
1 TTTG-ACCGGT
193323 TTTGACCGGT
1 TTTGACCGGT
193333 CTGAACTGGT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
9 25 0.38
10 31 0.48
11 9 0.14
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (10 bp):
TTTGACCGGT
Found at i:193280 original size:9 final size:9
Alignment explanation
Indices: 193243--193356 Score: 102
Period size: 9 Copynumber: 11.9 Consensus size: 9
193233 TTAGAAAACT
193243 GGTTTGACC
1 GGTTTGACC
193252 GGTTTTGAACC
1 GG-TTTG-ACC
*
193263 TGTTTTGACC
1 -GGTTTGACC
193273 GGTTTGACC
1 GGTTTGACC
*
193282 TGTTTTGACC
1 -GGTTTGACC
*
193292 GGTTTGATC
1 GGTTTGACC
193301 GGTTTCGACC
1 GGTTT-GACC
*
193311 GGTTCGAACC
1 GGTTTG-ACC
193321 GGTTTGACC
1 GGTTTGACC
* *
193330 GGTCTGAACT
1 GGTTTG-ACC
193340 GGTTTGACC
1 GGTTTGACC
*
193349 GGTCTGAC
1 GGTTTGAC
193357 TTGACCGTTG
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
9 40 0.47
10 37 0.44
11 7 0.08
12 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.30, T:0.35
Consensus pattern (9 bp):
GGTTTGACC
Found at i:193284 original size:19 final size:19
Alignment explanation
Indices: 193245--193356 Score: 109
Period size: 19 Copynumber: 5.8 Consensus size: 19
193235 AGAAAACTGG
193245 TTTGACCGGTTTTGAACCTGT
1 TTTGACCGG-TTTG-ACCTGT
193266 TTTGACCGGTTTGACCTGT
1 TTTGACCGGTTTGACCTGT
* *
193285 TTTGACCGGTTTGATCGGT
1 TTTGACCGGTTTGACCTGT
* * *
193304 TTCGACCGGTTCGAACC-GG
1 TTTGACCGGTTTG-ACCTGT
* * *
193323 TTTGACCGGTCTGAACTGG
1 TTTGACCGGTTTGACCTGT
*
193342 TTTGACCGGTCTGAC
1 TTTGACCGGTTTGAC
193357 TTGACCGTTG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
18 2 0.03
19 61 0.78
20 6 0.08
21 9 0.12
ACGTcount: A:0.13, C:0.22, G:0.29, T:0.36
Consensus pattern (19 bp):
TTTGACCGGTTTGACCTGT
Found at i:204684 original size:14 final size:13
Alignment explanation
Indices: 204654--204692 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
204644 AAAGTCAACG
*
204654 AGTTGACCCAGTA
1 AGTTGACTCAGTA
204667 AGTTGACTCAGCTA
1 AGTTGACTCAG-TA
204681 AGTTGACTCAGT
1 AGTTGACTCAGT
204693 GTGGATTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (13 bp):
AGTTGACTCAGTA
Found at i:206048 original size:30 final size:30
Alignment explanation
Indices: 205990--206048 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
205980 AAGTCAAAGT
*
205990 TCAACAGGTTGACTCGATCAAAGTCAACGG
1 TCAACAGGTTGACTCGATCAAAGCCAACGG
* *
206020 TCAATAGGTTGACTATG-TCAAAGCCAACG
1 TCAACAGGTTGACT-CGATCAAAGCCAACG
206049 AGCTGACCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (30 bp):
TCAACAGGTTGACTCGATCAAAGCCAACGG
Found at i:208478 original size:2 final size:2
Alignment explanation
Indices: 208471--208530 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
208461 ATAAACCATA
208471 AT AT AT 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
208513 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
208531 CACCAAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:211976 original size:23 final size:23
Alignment explanation
Indices: 211950--212018 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
211940 CACCACAGCT
* *
211950 CGTATAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
211973 CGTAGAATTACACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
211996 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
212019 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:212506 original size:2 final size:2
Alignment explanation
Indices: 212501--212554 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
212491 TACCTTATTC
212501 AT AT AT 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
212543 AT AT AT AT AT AT
1 AT AT AT AT AT AT
212555 CCGCAAATAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220877 original size:77 final size:79
Alignment explanation
Indices: 220776--220928 Score: 204
Period size: 77 Copynumber: 2.0 Consensus size: 79
220766 TTAATCAAAT
*
220776 TCTTATTTAATTAATTCAAATTAAATAACCATT-AAAGAATTATAATCTGAATTACA-CACTTTA
1 TCTTATTTAATTAATTCAAATTAAATAACCATTAAAAGAATTATAATCAGAATTACATCACTTTA
220839 ACGTTTATTTAAAC
66 ACGTTTATTTAAAC
* * * * * *
220853 TCTTATTTAATT-ATTCCGAATTAAATATCCATTAAAAGAGTTGTAATCAGAATTACATTATTTT
1 TCTTATTTAATTAATT-CAAATTAAATAACCATTAAAAGAATTATAATCAGAATTACATCACTTT
*
220917 AATGTTTATTTA
65 AACGTTTATTTA
220929 CTATATTCGA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
76 3 0.05
77 27 0.42
78 20 0.31
79 15 0.23
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (79 bp):
TCTTATTTAATTAATTCAAATTAAATAACCATTAAAAGAATTATAATCAGAATTACATCACTTTA
ACGTTTATTTAAAC
Found at i:224865 original size:17 final size:17
Alignment explanation
Indices: 224843--224877 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
224833 ATAATTTAAA
224843 ATTTTAATAATAAAAAT
1 ATTTTAATAATAAAAAT
* *
224860 ATTTTATTAATCAAAAT
1 ATTTTAATAATAAAAAT
224877 A
1 A
224878 AAATATAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTAATAATAAAAAT
Found at i:225829 original size:28 final size:28
Alignment explanation
Indices: 225777--225831 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
225767 GTTAACCAAA
* *
225777 TATCAATAAGACAGTATAACCGACCATT
1 TATCAATAAGACAGCAGAACCGACCATT
* *
225805 TATCAATTAGACAGCAGAACTGACCAT
1 TATCAATAAGACAGCAGAACCGACCAT
225832 ATAATAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.24
Consensus pattern (28 bp):
TATCAATAAGACAGCAGAACCGACCATT
Found at i:226289 original size:2 final size:2
Alignment explanation
Indices: 226282--226326 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
226272 GCATGCTGTC
226282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
226324 TA T
1 TA T
226327 GTATTATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:226433 original size:2 final size:2
Alignment explanation
Indices: 226426--226563 Score: 209
Period size: 2 Copynumber: 72.5 Consensus size: 2
226416 GTTTACGGTG
226426 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
226467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
226509 TA TA TA TA TA TA TA -A TA -A TA TA T- TA TA TA TA CA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
226547 TA T- TA TA T- TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA T
226564 GAGATGATGG
Statistics
Matches: 125, Mismatches: 4, Indels: 14
0.87 0.03 0.10
Matches are distributed among these distances:
1 7 0.06
2 118 0.94
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:227504 original size:2 final size:2
Alignment explanation
Indices: 227497--227527 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
227487 ATGCTAAACT
227497 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
227528 GTCAAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:229116 original size:28 final size:28
Alignment explanation
Indices: 229042--229118 Score: 136
Period size: 28 Copynumber: 2.8 Consensus size: 28
229032 AAAGGACCAC
*
229042 TATGTCCCGAAGGACCACATAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
229070 TATGTCCCGAAGGACCACGTAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
*
229098 TATGTCCTGAAGGACCACGTA
1 TATGTCCCGAAGGACCACGTA
229119 TAACCCTCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACGTAGAACACA
Found at i:232526 original size:3 final size:3
Alignment explanation
Indices: 232518--232596 Score: 131
Period size: 3 Copynumber: 26.3 Consensus size: 3
232508 CTGCATTAAA
* * *
232518 AAT AAT AAT ATT AAT AAT ACT AAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
232566 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
232597 GCAGGACGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:234194 original size:27 final size:28
Alignment explanation
Indices: 234164--234227 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
234154 TAAAATATAA
234164 ATTATTTTTAATGTATTTTTA-TT-AAAT
1 ATTATTTTT-ATGTATTTTTATTTAAAAT
***
234191 ATTATAAATATGTATTTTTATTTAAAAT
1 ATTATTTTTATGTATTTTTATTTAAAAT
234219 ATGTATTTT
1 AT-TATTTT
234228 AAAACACATG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
26 11 0.39
27 8 0.29
28 6 0.21
29 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (28 bp):
ATTATTTTTATGTATTTTTATTTAAAAT
Done.