Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 127 of 135
Found at i:38620848 original size:56 final size:57
Alignment explanation
Indices: 38620711--38620849 Score: 160
Period size: 55 Copynumber: 2.5 Consensus size: 57
38620701 TATATTATTG
* * *
38620711 TTTTGGTGCTGTTTTT-TTTACTATTTTGGTTGCTATTTTTTACTGTTTTGATGTTGT
1 TTTTGTTGCTGTTTTTGTTT-CTATTTTGGATGCTATTTTTTACTGTTTTGATGTTAT
** * *
38620768 TTTT-TTATTG-TTTTGATTACTATTTT-GATGCTTTTTTTTACTGTTTTGATGTTAT
1 TTTTGTTGCTGTTTTTG-TTTCTATTTTGGATGCTATTTTTTACTGTTTTGATGTTAT
*
38620823 TTTTGTTGCTGTTTTTGTTTTTATTTT
1 TTTTGTTGCTGTTTTTGTTTCTATTTT
38620850 TGTTATTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
55 34 0.51
56 22 0.33
57 11 0.16
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.68
Consensus pattern (57 bp):
TTTTGTTGCTGTTTTTGTTTCTATTTTGGATGCTATTTTTTACTGTTTTGATGTTAT
Found at i:38620850 original size:44 final size:44
Alignment explanation
Indices: 38620802--38620914 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 44
38620792 TTGATGCTTT
* * * * *
38620802 TTTTTACTGTTTTGATGTTATTTTTGTTGCTGTTTTTGTTTTTA
1 TTTTTATTGTTTTGATGTTATTTTTGCTGCTATTTTGGTTGTTA
* *
38620846 TTTTTGTTATTTT-ACTGTTATTTTTGCTGCTATTTTGGTTGTTA
1 TTTTTATTGTTTTGA-TGTTATTTTTGCTGCTATTTTGGTTGTTA
* * *
38620890 ATTTGATTGTTTGGATGTTATTTTT
1 TTTTTATTGTTTTGATGTTATTTTT
38620915 ATACGCTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
43 1 0.02
44 53 0.96
45 1 0.02
ACGTcount: A:0.12, C:0.04, G:0.17, T:0.67
Consensus pattern (44 bp):
TTTTTATTGTTTTGATGTTATTTTTGCTGCTATTTTGGTTGTTA
Found at i:38622068 original size:30 final size:31
Alignment explanation
Indices: 38622034--38622091 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
38622024 TATACAATGT
*
38622034 TAAAATATGTAA-TT-AGTCCCTATACTTTGA
1 TAAAATATG-AACTTCAGTCCATATACTTTGA
*
38622064 TAAAATTTGAACTTCAGTCCATATACTT
1 TAAAATATGAACTTCAGTCCATATACTT
38622092 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 10 0.42
31 12 0.50
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (31 bp):
TAAAATATGAACTTCAGTCCATATACTTTGA
Found at i:38622784 original size:49 final size:49
Alignment explanation
Indices: 38622692--38622785 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
38622682 TATTTACAGA
* ** *
38622692 TTGAAAACCCTTATTCTAATAAATGTCAAATAGATGAAGTGTAGTAAAG
1 TTGAAAAACCTTATTCTAATAAATGTCAAATAGAAAAAATGTAGTAAAG
38622741 TTGAAAAACCTTATTCTAATAAATGTCAAATAGAAAAAATGTAGT
1 TTGAAAAACCTTATTCTAATAAATGTCAAATAGAAAAAATGTAGT
38622786 TCTGTACGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.31
Consensus pattern (49 bp):
TTGAAAAACCTTATTCTAATAAATGTCAAATAGAAAAAATGTAGTAAAG
Found at i:38628334 original size:2 final size:2
Alignment explanation
Indices: 38628329--38628353 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38628319 TTTCTCTCTC
38628329 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
38628354 TTTTATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38635165 original size:25 final size:26
Alignment explanation
Indices: 38635115--38635166 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
38635105 AAAATATTTG
*
38635115 AGGTGAAAAATTTGAGAATTTCAATA
1 AGGTGAAAAATTTGAGAACTTCAATA
38635141 AGGTGAAAAATTTGAGAACTT-AATA
1 AGGTGAAAAATTTGAGAACTTCAATA
38635166 A
1 A
38635167 TTTAACAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.29
Consensus pattern (26 bp):
AGGTGAAAAATTTGAGAACTTCAATA
Found at i:38636075 original size:24 final size:25
Alignment explanation
Indices: 38636033--38636103 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
38636023 GTGTGGTAGT
*
38636033 GAAGCT-TTTCGAGATGGAG-GGGAG
1 GAAGCTGTTTC-AGAGGGAGAGGGAG
38636057 GAAGCTGTTTCAGAGGGAGACAGGGAG
1 GAAGCTGTTTCAGAGGGAG--AGGGAG
* *
38636084 GAAGTTGTTTTAGAGGGAGA
1 GAAGCTGTTTCAGAGGGAGA
38636104 TAATGATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 13 0.32
25 5 0.12
27 22 0.55
ACGTcount: A:0.28, C:0.07, G:0.44, T:0.21
Consensus pattern (25 bp):
GAAGCTGTTTCAGAGGGAGAGGGAG
Found at i:38636086 original size:27 final size:27
Alignment explanation
Indices: 38636052--38636103 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
38636042 CGAGATGGAG
38636052 GGGAGGAAGCTGTTTCAGAGGGAGACA
1 GGGAGGAAGCTGTTTCAGAGGGAGACA
* *
38636079 GGGAGGAAGTTGTTTTAGAGGGAGA
1 GGGAGGAAGCTGTTTCAGAGGGAGA
38636104 TAATGATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.06, G:0.46, T:0.19
Consensus pattern (27 bp):
GGGAGGAAGCTGTTTCAGAGGGAGACA
Found at i:38638777 original size:52 final size:52
Alignment explanation
Indices: 38638696--38638882 Score: 304
Period size: 52 Copynumber: 3.6 Consensus size: 52
38638686 TTCTCATTTA
* * *
38638696 ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGAAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
*
38638748 ATACTCACGATGACACATAATCATCGAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
*
38638800 ATACTCACGATGACACATAGTCAT-TAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGA-ACCTCATAATCCGTAAAGGATTCAT
*
38638852 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGAACCT
38638883 TTTGCATTTA
Statistics
Matches: 125, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
51 1 0.01
52 124 0.99
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
Found at i:38644706 original size:17 final size:17
Alignment explanation
Indices: 38644684--38644719 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
38644674 TTAAAATTAT
38644684 TTTTTTAAAATATAAAA
1 TTTTTTAAAATATAAAA
38644701 TTTTTTAAAATATAAAA
1 TTTTTTAAAATATAAAA
38644718 TT
1 TT
38644720 ATTAAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTTAAAATATAAAA
Found at i:38646833 original size:30 final size:30
Alignment explanation
Indices: 38646779--38647008 Score: 162
Period size: 29 Copynumber: 7.8 Consensus size: 30
38646769 ACTTTTGGAT
*
38646779 AATCGAGGGT-AAAATGGTAA-TTTTGGTGA
1 AATCGAGGTTAAAAATGG-AATTTTTGGTGA
*
38646808 AATCGAGGTTAAAAATAGAATTTTTGAG-G-
1 AATCGAGGTTAAAAATGGAATTTTTG-GTGA
** * * *
38646837 CTTCGAGGGT-AATATGGTAATTTTTGATGA
1 AATCGAGGTTAAAAATGG-AATTTTTGGTGA
*
38646867 AATCGAGGTTAAAAATGGGA-TTTT-G-GA
1 AATCGAGGTTAAAAATGGAATTTTTGGTGA
* * *
38646894 AAGTTTGAGGGT-AAAATGGTAATTTTTAGTGA
1 AA--TCGAGGTTAAAAATGG-AATTTTTGGTGA
38646926 AATCGAGGTTAAAAATGGAA-TTTT-G-GA
1 AATCGAGGTTAAAAATGGAATTTTTGGTGA
* *
38646953 AATTTCGGGGGT-AAAATGGTAATTTTTGGTGA
1 AA--TCGAGGTTAAAAATGG-AATTTTTGGTGA
*
38646985 AATCGGGGTTAAAAATGGAATTTT
1 AATCGAGGTTAAAAATGGAATTTT
38647009 GGAAAGTTCG
Statistics
Matches: 158, Mismatches: 22, Indels: 41
0.71 0.10 0.19
Matches are distributed among these distances:
27 8 0.05
28 20 0.13
29 50 0.32
30 49 0.31
31 23 0.15
32 8 0.05
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
AATCGAGGTTAAAAATGGAATTTTTGGTGA
Found at i:38646890 original size:59 final size:59
Alignment explanation
Indices: 38646747--38647156 Score: 476
Period size: 59 Copynumber: 7.0 Consensus size: 59
38646737 TAAGAAACGA
* ** *
38646747 TGAAATCGGGGTTGAAAACGGGACTTTTGGATAA--TCGAGGGTAAAATGGTAA-TTTTGG
1 TGAAATCGAGGTT-AAAAATGGAATTTTGGA-AAGTTCGAGGGTAAAATGGTAATTTTTGG
* * * * *
38646805 TGAAATCGAGGTTAAAAATAGAATTTTTG-AGGCTTCGAGGGTAATATGGTAATTTTTGA
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAG-TTCGAGGGTAAAATGGTAATTTTTGG
* * *
38646864 TGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTAG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
* *
38646923 TGAAATCGAGGTTAAAAATGGAATTTTGGAAATTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
*
38646982 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCG-GTGGTAAAATGGTAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAG-GGTAAAATGGTAATTTTTGG
* * * * * *
38647041 TAAAATC-AGGGTT-AAAATGGAATCTTAGAAAGTTTGGGGGTAAAATGGTATTTTTTGG
1 TGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
* * * * * *
38647099 TAAAATCGGGGTT-AAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
38647157 AAGTTTCGGG
Statistics
Matches: 309, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.00
57 11 0.04
58 122 0.39
59 173 0.56
60 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
Found at i:38647057 original size:30 final size:29
Alignment explanation
Indices: 38646749--38647124 Score: 181
Period size: 30 Copynumber: 12.8 Consensus size: 29
38646739 AGAAACGATG
* * *
38646749 AAATCGGGGTTGAAAACGGGACTTTTGG-A
1 AAATCGGGGTT-AAAATGGAATTTTTGGTA
* *
38646778 TAATCGAGGG-TAAAATGGTAA-TTTTGGTG
1 AAATCG-GGGTTAAAATGG-AATTTTTGGTA
* *
38646807 AAATCGAGGTTAAAAATAGAATTTTT-G-A
1 AAATCGGGGTT-AAAATGGAATTTTTGGTA
*** * * *
38646835 GGCTTCGAGGG-TAATATGGTAATTTTTGATG
1 -AAATCG-GGGTTAAAATGG-AATTTTTGGTA
* *
38646866 AAATCGAGGTTAAAAATGGGA-TTTTGG-A
1 AAATCGGGGTT-AAAATGGAATTTTTGGTA
* * * *
38646894 AAGTTTGAGGG-TAAAATGGTAATTTTTAGTG
1 AA-ATCG-GGGTTAAAATGG-AATTTTTGGTA
*
38646925 AAATCGAGGTTAAAAATGGAA-TTTTGG-A
1 AAATCGGGGTT-AAAATGGAATTTTTGGTA
* * *
38646953 AATTTCGGGGGTAAAATGGTAATTTTTGGTG
1 AA-ATCGGGGTTAAAATGG-AATTTTTGGTA
38646984 AAATCGGGGTTAAAAATGGAA-TTTTGG-A
1 AAATCGGGGTT-AAAATGGAATTTTTGGTA
*
38647012 AAGTTCGGTGG-TAAAATGGTAATTTTTGGTA
1 AA-ATCGG-GGTTAAAATGG-AATTTTTGGTA
* * *
38647043 AAATCAGGGTTAAAATGGAA-TCTTAG-A
1 AAATCGGGGTTAAAATGGAATTTTTGGTA
* * * *
38647070 AAGTTTGGGGGTAAAATGGTATTTTTTGGTA
1 AA-ATCGGGGTTAAAATGG-AATTTTTGGTA
38647101 AAATCGGGGTTAAAATGGAATTTT
1 AAATCGGGGTTAAAATGGAATTTT
38647125 AGAAGGTTTG
Statistics
Matches: 254, Mismatches: 58, Indels: 70
0.66 0.15 0.18
Matches are distributed among these distances:
27 3 0.01
28 62 0.24
29 76 0.30
30 83 0.33
31 30 0.12
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
AAATCGGGGTTAAAATGGAATTTTTGGTA
Found at i:38647142 original size:28 final size:28
Alignment explanation
Indices: 38646937--38647167 Score: 94
Period size: 30 Copynumber: 8.0 Consensus size: 28
38646927 ATCGAGGTTA
* *
38646937 AAAATGG-AATTTTGGAAATTTCGGGGGT
1 AAAATGGTAATTTTAGAAGTTT-GGGGGT
* * * *
38646965 AAAATGGTAATTTTTGGTGAA-ATCGGGGTT
1 AAAATGGTAA-TTTT--AGAAGTTTGGGGGT
* * *
38646995 AAAAATGG-AATTTTGGAAAGTTCGGTGGT
1 -AAAATGGTAATTTTAG-AAGTTTGGGGGT
* ** ** *
38647024 AAAATGGTAATTTTTGGTAAAATCAGGGTT
1 AAAATGGTAA-TTTTAG-AAGTTTGGGGGT
*
38647054 AAAATGG-AATCTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTAG-AAGTTTGGGGGT
* * ** * *
38647082 AAAATGGTATTTTTTGGTAAAATCGGGGTT
1 AAAATGGTA-ATTTTAG-AAGTTTGGGGGT
38647112 AAAATGG-AATTTTAGAAGGTTTGGGGGT
1 AAAATGGTAATTTTAGAA-GTTTGGGGGT
* *
38647140 AAAATGGTAATTTTTGGAAGTTTCGGGG
1 AAAATGGTAA-TTTTAGAAGTTTGGGGG
38647168 ACCTATAAAT
Statistics
Matches: 151, Mismatches: 38, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
27 3 0.02
28 52 0.34
29 28 0.19
30 57 0.38
31 8 0.05
32 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (28 bp):
AAAATGGTAATTTTAGAAGTTTGGGGGT
Found at i:38647431 original size:163 final size:162
Alignment explanation
Indices: 38647227--38647561 Score: 528
Period size: 163 Copynumber: 2.1 Consensus size: 162
38647217 AGCATCCAGC
* * * * * *
38647227 AGTCAAGGGATTAAATTGTAAACCTTGAAAAATTCTTGGGCCAATTTTATAATTAAATAAGAGTT
1 AGTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGGCCAATTTTATAATTAAATAAAAGTT
* * *
38647292 GATTTGGGGATTAAATTAAAACAAATTCAAAATGTCAGGGACTAAATGAATAAATAAGCTAAAAA
66 GATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAAA
*
38647357 GTGACACGTGGCAGCCCCCTGGTGCAGTCAAACT
131 ATGACACGTGGCAGCCCCC-GGTGCAGTCAAA-T
*
38647391 -GTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGGCCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGGCCAATTTTATAATTAAATAAAAGTT
38647455 GATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAAA
66 GATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAAA
* *
38647520 ATGACACGTGGCAGCCTCCGGTGCAGTCCAAT
131 ATGACACGTGGCAGCCCCCGGTGCAGTCAAAT
38647552 AGTCAAAGGA
1 AGTCAAAGGA
38647562 TTAAATTGAA
Statistics
Matches: 157, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
161 1 0.01
162 20 0.13
163 136 0.87
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (162 bp):
AGTCAAAGGACTAATTTATAAACCTTGAAAAATTATTGGGCCAATTTTATAATTAAATAAAAGTT
GATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAAA
ATGACACGTGGCAGCCCCCGGTGCAGTCAAAT
Found at i:38649257 original size:6 final size:6
Alignment explanation
Indices: 38649246--38649326 Score: 82
Period size: 6 Copynumber: 13.8 Consensus size: 6
38649236 TTAATATCAT
*
38649246 TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
38649291 TAAATAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTAA
1 T--TTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
38649327 TAAAATTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
4 3 0.05
5 11 0.17
6 43 0.68
7 1 0.02
8 5 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:38649261 original size:23 final size:22
Alignment explanation
Indices: 38649246--38649326 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 22
38649236 TTAATATCAT
38649246 TTTAAATTTAAATTTAATTAAA
1 TTTAAATTTAAATTTAATTAAA
* *
38649268 TTTAAATTTAAAATAAATTTAAA
1 TTTAAATTTAAATTTAA-TTAAA
* *
38649291 TAAATAAATTTAAATTTAAGATAAA
1 T--TTAAATTTAAATTTAA-TTAAA
38649316 TTTAAATTTAA
1 TTTAAATTTAA
38649327 TAAAATTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
22 15 0.31
23 15 0.31
25 18 0.38
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (22 bp):
TTTAAATTTAAATTTAATTAAA
Found at i:38649266 original size:16 final size:16
Alignment explanation
Indices: 38649247--38649347 Score: 125
Period size: 16 Copynumber: 6.3 Consensus size: 16
38649237 TAATATCATT
38649247 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAA
38649263 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTT-AA
*
38649280 ATAAATTTAAA--TAA
1 TTAAATTTAAATTTAA
*
38649294 ATAAATTTAAATTTAA
1 TTAAATTTAAATTTAA
*
38649310 GATAAATTTAAATTTAA
1 -TTAAATTTAAATTTAA
* *
38649327 TAAAATTTAAAATTAA
1 TTAAATTTAAATTTAA
38649343 TTAAA
1 TTAAA
38649348 AAATTAAAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
14 13 0.17
15 1 0.01
16 34 0.45
17 28 0.37
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAATTTAA
Found at i:38649286 original size:17 final size:17
Alignment explanation
Indices: 38649248--38649342 Score: 119
Period size: 17 Copynumber: 5.9 Consensus size: 17
38649238 AATATCATTT
*
38649248 TAAATTTAAATTT-AAT
1 TAAATTTAAATTTAAAA
38649264 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
38649281 TAAATTTAAA--T-AAA
1 TAAATTTAAATTTAAAA
*
38649295 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
*
38649312 TAAATTTAAATTTAATA
1 TAAATTTAAATTTAAAA
*
38649329 -AAATTTAAAATTAA
1 TAAATTTAAATTTAA
38649343 TTAAAAAATT
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.18
15 1 0.01
16 27 0.38
17 30 0.42
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:38649299 original size:47 final size:47
Alignment explanation
Indices: 38649248--38649337 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
38649238 AATATCATTT
*
38649248 TAAATTTAAATTTAA-TTAAATTTAAATTTAAAATAAATTTAAATAAA
1 TAAATTTAAATTTAAGATAAATTTAAATTTAAAA-AAATTTAAATAAA
*
38649295 TAAATTTAAATTTAAGATAAATTTAAATTTAATAAAATTTAAA
1 TAAATTTAAATTTAAGATAAATTTAAATTTAAAAAAATTTAAA
38649338 ATTAATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
47 24 0.60
48 16 0.40
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (47 bp):
TAAATTTAAATTTAAGATAAATTTAAATTTAAAAAAATTTAAATAAA
Found at i:38653293 original size:29 final size:29
Alignment explanation
Indices: 38653225--38653581 Score: 151
Period size: 29 Copynumber: 12.4 Consensus size: 29
38653215 GTAAAAAAAA
*
38653225 AGGGGTTAAAATG-AAGTTTT-GAAGAG-TT
1 AGGGGCTAAAATGTAA-TTTTGGAA-AGTTT
* * *
38653253 CGGGGTTAAAATGTAATTTTGGAAAATTTT
1 AGGGGCTAAAATGTAATTTTGG-AAAGTTT
* * * *
38653283 AGGGG-TAAAATATCATTTTGGGAGAGTTC
1 AGGGGCTAAAATGTAATTTT-GGAAAGTTT
*
38653312 A-GGG-TAAAAATGTGATTTTTGG-AAGTTT
1 AGGGGCT-AAAATGT-AATTTTGGAAAGTTT
* * *
38653340 GGGGGCAAAAATGTAAGTTTTGG-AAG-AT
1 AGGGGCTAAAATGTAA-TTTTGGAAAGTTT
* * *
38653368 CGGGG-TAAAAATGCGATTTTTGG-AAGTTT
1 AGGGGCT-AAAATG-TAATTTTGGAAAGTTT
* * *
38653397 TGGAG-TAAAAATGTGATTTTTGG-AAGTTT
1 AGGGGCT-AAAATGT-AATTTTGGAAAGTTT
*
38653426 AGGGGCAAAAATGTAATTTTGG-AAG-TT
1 AGGGGCTAAAATGTAATTTTGGAAAGTTT
* *
38653453 AGGGGGCAAAAATGTAATTTTTGAGAAG-TT
1 A-GGGGCTAAAATGTAATTTTGGA-AAGTTT
* * * *
38653483 CGAGGG-TAAAATGTGATTTCT-GTAAG-CT
1 AG-GGGCTAAAATGTAATTT-TGGAAAGTTT
*
38653511 AGGGGC-AAAATGCAATTTTGGAAAAGTTT
1 AGGGGCTAAAATGTAATTTTGG-AAAGTTT
* * *
38653540 GGGGGTTAAAATGTAATTTTAGAAAAGTTT
1 AGGGGCTAAAATGTAATTTT-GGAAAGTTT
*
38653570 AGGGGTTAAAAT
1 AGGGGCTAAAAT
38653582 ATGATTTCTA
Statistics
Matches: 258, Mismatches: 45, Indels: 50
0.73 0.13 0.14
Matches are distributed among these distances:
26 1 0.00
27 17 0.07
28 83 0.32
29 103 0.40
30 53 0.21
31 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AGGGGCTAAAATGTAATTTTGGAAAGTTT
Found at i:38653386 original size:57 final size:57
Alignment explanation
Indices: 38653232--38653501 Score: 244
Period size: 57 Copynumber: 4.7 Consensus size: 57
38653222 AAAAGGGGTT
* * * * * * *
38653232 AAAATG-AAGTTTTGAAGAGTTCGGGGTTAAAATGT-AATTTTGGAAAATTTTAGGGG-T
1 AAAATGTAATTTTTGGA-AGTTCGGGGTAAAAATGTGATTTTTGG--AAGTTTGGGGGCA
* * * *
38653289 AAAATATCATTTTGGGAGAGTTCAGGGTAAAAATGTGATTTTTGGAAGTTTGGGGGCA
1 AAAATGTAATTTTTGGA-AGTTCGGGGTAAAAATGTGATTTTTGGAAGTTTGGGGGCA
* * * * * *
38653347 AAAATGTAAGTTTTGGAAGATCGGGGTAAAAATGCGATTTTTGGAAGTTTTGGAGTA
1 AAAATGTAATTTTTGGAAGTTCGGGGTAAAAATGTGATTTTTGGAAGTTTGGGGGCA
* * * * *
38653404 AAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATGT-AATTTTGGAAGTTAGGGGGCA
1 AAAATGTAATTTTTGGAAG-TTCGGGGTAAAAATGTGATTTTTGGAAGTTTGGGGGCA
38653461 AAAATGTAATTTTTGAGAAGTTCGAGGGT-AAAATGTGATTT
1 AAAATGTAATTTTTG-GAAGTTCG-GGGTAAAAATGTGATTT
38653502 CTGTAAGCTA
Statistics
Matches: 170, Mismatches: 36, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
57 105 0.62
58 58 0.34
59 7 0.04
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTCGGGGTAAAAATGTGATTTTTGGAAGTTTGGGGGCA
Found at i:38653387 original size:86 final size:84
Alignment explanation
Indices: 38653260--38653533 Score: 274
Period size: 86 Copynumber: 3.2 Consensus size: 84
38653250 GTTCGGGGTT
*
38653260 AAAATGTAATTTTGGAAAATTTTA-GGGGTAAAATAT-CATTTTGGGAGAGTTCAGGGTAAAAAT
1 AAAATGTAATTTTGGAAGA---TACGGGGTAAAA-ATGCATTTT-GGAGAGTTCAGGGTAAAAAT
*
38653323 GTGATTTTTGGAAGTTTGGGGGCA
61 GTGATTTTTGGAAGTTTAGGGGCA
**
38653347 AAAATGTAAGTTTTGGAAGAT-CGGGGTAAAAATGCGATTTTTGGA-AGTTTTGGAGTAAAAATG
1 AAAATGTAA-TTTTGGAAGATACGGGGTAAAAATGC-A-TTTTGGAGAGTTCAGG-GTAAAAATG
38653410 TGATTTTTGGAAGTTTAGGGGCA
62 TGATTTTTGGAAGTTTAGGGGCA
* * * * *
38653433 AAAATGTAATTTTGGAAGTTAGGGGGCAAAAATGTAATTTTTGAGAAGTTCGAGGGT-AAAATGT
1 AAAATGTAATTTTGGAAGATACGGGGTAAAAATG-CATTTTGGAG-AGTTC-AGGGTAAAAATGT
* * *
38653497 GATTTCTGTAAG-CTAGGGGC-
63 GATTTTTGGAAGTTTAGGGGCA
*
38653517 AAAATGCAATTTTGGAA
1 AAAATGTAATTTTGGAA
38653534 AAGTTTGGGG
Statistics
Matches: 161, Mismatches: 15, Indels: 25
0.80 0.07 0.12
Matches are distributed among these distances:
84 18 0.11
85 40 0.25
86 73 0.45
87 19 0.12
88 11 0.07
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (84 bp):
AAAATGTAATTTTGGAAGATACGGGGTAAAAATGCATTTTGGAGAGTTCAGGGTAAAAATGTGAT
TTTTGGAAGTTTAGGGGCA
Found at i:38653516 original size:57 final size:57
Alignment explanation
Indices: 38653232--38653574 Score: 215
Period size: 57 Copynumber: 6.0 Consensus size: 57
38653222 AAAAGGGGTT
* * * * *
38653232 AAAATG-AAGTTTTGAAGAGTTCG-GGGTTAAAATGT-AATTTTGGAAAATTTTAGGGG-T
1 AAAATGTAATTTTTGGA-AGTTCGAGGG-TAAAATGTGATTTTTGG--AAGTTTAGGGGCA
* * * *
38653289 AAAATATCATTTTGGGAGAGTTC-AGGGTAAAAATGTGATTTTTGGAAGTTTGGGGGCA
1 AAAATGTAATTTTTGGA-AGTTCGAGGGT-AAAATGTGATTTTTGGAAGTTTAGGGGCA
* * * * * *
38653347 AAAATGTAAGTTTTGGAAGATCG-GGGTAAAAATGCGATTTTTGGAAGTTTTGGAGTA
1 AAAATGTAATTTTTGGAAGTTCGAGGGT-AAAATGTGATTTTTGGAAGTTTAGGGGCA
* * * *
38653404 AAAATGTGATTTTTGGAAGTT-TAGGGGCAAAAATGT-AATTTTGGAAG-TTAGGGGGCA
1 AAAATGTAATTTTTGGAAGTTCGA-GGG-TAAAATGTGATTTTTGGAAGTTTA-GGGGCA
* * *
38653461 AAAATGTAATTTTTGAGAAGTTCGAGGGTAAAATGTGATTTCTGTAAG-CTAGGGGC-
1 AAAATGTAATTTTTG-GAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTTAGGGGCA
* * * * * *
38653517 AAAATGCAA-TTTTGGAAAAGTTTGGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGG
1 AAAATGTAATTTTTGG--AAGTTCGAGGG-TAAAATGTGATTTTTG-GAAGTTTAGGGG
38653575 TTAAAATATG
Statistics
Matches: 225, Mismatches: 43, Indels: 34
0.75 0.14 0.11
Matches are distributed among these distances:
54 1 0.00
55 5 0.02
56 19 0.08
57 120 0.53
58 66 0.29
59 14 0.06
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTTAGGGGCA
Found at i:38653538 original size:86 final size:87
Alignment explanation
Indices: 38653313--38653590 Score: 235
Period size: 86 Copynumber: 3.2 Consensus size: 87
38653303 GGAGAGTTCA
* * * * * * * *
38653313 GGGTAAAAATGTGATTTTTGGAAGTTTGGGGGCAAAAATGTAAGTTTTGGAAGAT-CGGGGTAAA
1 GGGTTAAAATGTGATTTCTGGAAGTCTAGGGGCAAAAATGCAA-TTTTGGAAGTTAGGGGGCAAA
** * * **
38653377 AATGCGATTTTTG-GAAGTTTTG
65 AATGTAATTTTAGAAAAGTTGAG
* * * * *
38653399 GAGTAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTTGGAAGTTAGGGGGCAAAA
1 GGGTTAAAATGTGATTTCTGGAAGTCTAGGGGCAAAAATGCAATTTTGGAAGTTAGGGGGCAAAA
* *
38653464 ATGTAATTTTTGAGAAGTTCGA-
66 ATGTAATTTTAGAAAAGTT-GAG
* * **
38653486 GGG-TAAAATGTGATTTCTGTAAG-CTAGGGGC-AAAATGCAATTTTGGAAAAGTTTGGGGGTTA
1 GGGTTAAAATGTGATTTCTGGAAGTCTAGGGGCAAAAATGCAATTTTGG--AAGTTAGGGGGCAA
*
38653548 AAATGTAATTTTAGAAAAGTTTAG
64 AAATGTAATTTTAGAAAAGTTGAG
*
38653572 GGGTTAAAATATGATTTCT
1 GGGTTAAAATGTGATTTCT
38653591 AAAAAGTTTA
Statistics
Matches: 163, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
84 14 0.09
85 18 0.11
86 109 0.67
87 22 0.13
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (87 bp):
GGGTTAAAATGTGATTTCTGGAAGTCTAGGGGCAAAAATGCAATTTTGGAAGTTAGGGGGCAAAA
ATGTAATTTTAGAAAAGTTGAG
Found at i:38653551 original size:30 final size:30
Alignment explanation
Indices: 38653517--38653581 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
38653507 AGCTAGGGGC
* *
38653517 AAAATGCAATTTTGGAAAAGTTTGGGGGTT
1 AAAATGCAATTTTAGAAAAGTTTAGGGGTT
*
38653547 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
1 AAAATGCAATTTTAGAAAAGTTTAGGGGTT
38653577 AAAAT
1 AAAAT
38653582 ATGATTTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.34
Consensus pattern (30 bp):
AAAATGCAATTTTAGAAAAGTTTAGGGGTT
Found at i:38653596 original size:30 final size:30
Alignment explanation
Indices: 38653524--38653600 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
38653514 GGCAAAATGC
* * *
38653524 AATTTTGGAAAAGTTTGGGGGTTAAAATGT
1 AATTTTAGAAAAGTTTAGGGGTTAAAATAT
38653554 AATTTTAGAAAAGTTTAGGGGTTAAAATAT
1 AATTTTAGAAAAGTTTAGGGGTTAAAATAT
*
38653584 GATTTCTA-AAAAGTTTA
1 AATTT-TAGAAAAGTTTA
38653601 AGGACCTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 40 0.95
31 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.38
Consensus pattern (30 bp):
AATTTTAGAAAAGTTTAGGGGTTAAAATAT
Found at i:38654731 original size:10 final size:10
Alignment explanation
Indices: 38654716--38654750 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
38654706 ACTATTATTG
38654716 TTATTATTAT
1 TTATTATTAT
38654726 TTATTATTAT
1 TTATTATTAT
*
38654736 TTAATATTAT
1 TTATTATTAT
*
38654746 ATATT
1 TTATT
38654751 TAATGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTATTAT
Found at i:38662004 original size:19 final size:17
Alignment explanation
Indices: 38661982--38662029 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
38661972 CATTAAATAA
*
38661982 AATTATTTTAATTTCATGT
1 AATTATTTT-ATTT-ATAT
*
38662001 AATTACTTTATTTATAT
1 AATTATTTTATTTATAT
*
38662018 AATTATGTTATT
1 AATTATTTTATT
38662030 ATAAGTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 13 0.52
18 4 0.16
19 8 0.32
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (17 bp):
AATTATTTTATTTATAT
Found at i:38665771 original size:2 final size:2
Alignment explanation
Indices: 38665729--38665760 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38665719 AATATCAATA
38665729 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
38665761 TATTGATATA
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:38667859 original size:2 final size:2
Alignment explanation
Indices: 38667852--38667880 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38667842 AAGGAAGGTA
38667852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38667881 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38667885 original size:2 final size:2
Alignment explanation
Indices: 38667880--38667912 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38667870 ATATATATAT
38667880 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38667913 TAATACCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38668162 original size:17 final size:18
Alignment explanation
Indices: 38668137--38668170 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38668127 AAGAAGAAGG
*
38668137 ATTTGTAGTG-GGGTGAT
1 ATTTATAGTGTGGGTGAT
38668154 ATTTATAGTGTGGGTGA
1 ATTTATAGTGTGGGTGA
38668171 GGATTAACTA
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:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (18 bp):
ATTTATAGTGTGGGTGAT
Found at i:38671807 original size:18 final size:18
Alignment explanation
Indices: 38671784--38671818 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38671774 AAAATTAAAT
*
38671784 CTATTGTATTATCTTATA
1 CTATTGTATTATATTATA
38671802 CTATTGTATTATATTAT
1 CTATTGTATTATATTAT
38671819 GTTTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (18 bp):
CTATTGTATTATATTATA
Found at i:38675468 original size:23 final size:22
Alignment explanation
Indices: 38675418--38675478 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
38675408 GAAGGTTAAA
* *
38675418 ATTAAATTATAATTTTTATAAT
1 ATTAAATTATAATTTTTAAAAG
*
38675440 AGTAAATATATAATTTTTAAAAG
1 ATTAAAT-TATAATTTTTAAAAG
*
38675463 ATTAAATTAAAATTTT
1 ATTAAATTATAATTTT
38675479 ATTATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
ATTAAATTATAATTTTTAAAAG
Found at i:38675508 original size:31 final size:30
Alignment explanation
Indices: 38675452--38675520 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
38675442 TAAATATATA
*
38675452 ATTTTTAAAAGATTAAATTAAAATTTTATT
1 ATTTTTAAAAGATTAAAATAAAATTTTATT
*
38675482 ATTTTTAAGGAAG-TTAAAATATAATTTTATT
1 ATTTTTAA--AAGATTAAAATAAAATTTTATT
38675513 -TTTATTAA
1 ATTT-TTAA
38675521 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 11 0.32
31 20 0.59
32 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (30 bp):
ATTTTTAAAAGATTAAAATAAAATTTTATT
Found at i:38699409 original size:18 final size:19
Alignment explanation
Indices: 38699374--38699414 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
38699364 ATTAAATAGT
*
38699374 TCGAGTTATTTGAGTTAA-
1 TCGAGTTATTAGAGTTAAC
38699392 TCGAGTTATTCAGA-TTAAC
1 TCGAGTTATT-AGAGTTAAC
38699411 TCGA
1 TCGA
38699415 ATAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (19 bp):
TCGAGTTATTAGAGTTAAC
Found at i:38700334 original size:16 final size:16
Alignment explanation
Indices: 38700313--38700361 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
38700303 TTGATAAATT
* *
38700313 AAAAAATTAAGTGTTG
1 AAAAAATTAAGTATTA
*
38700329 AAAAAA-TAAATATTA
1 AAAAAATTAAGTATTA
38700344 AAAAAATTAAGTACTTA
1 AAAAAATTAAGTA-TTA
38700361 A
1 A
38700362 TTTAAGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 12 0.44
16 11 0.41
17 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (16 bp):
AAAAAATTAAGTATTA
Found at i:38700552 original size:15 final size:14
Alignment explanation
Indices: 38700531--38700563 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
38700521 TTCTACATTT
38700531 TTTTATA-AAAAAA
1 TTTTATATAAAAAA
*
38700544 TTTTATATAATAAA
1 TTTTATATAAAAAA
38700558 TTTTAT
1 TTTTAT
38700564 TGTGTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTATATAAAAAA
Found at i:38700601 original size:16 final size:17
Alignment explanation
Indices: 38700577--38700611 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38700567 GTGTTATTAA
38700577 AAGTGTCTAAAAA-ATT
1 AAGTGTCTAAAAATATT
*
38700593 AAGTTTCTAAAAATATT
1 AAGTGTCTAAAAATATT
38700610 AA
1 AA
38700612 TATTCAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (17 bp):
AAGTGTCTAAAAATATT
Found at i:38702976 original size:22 final size:22
Alignment explanation
Indices: 38702941--38702983 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38702931 TTTTCTTTTC
*
38702941 TTTTACTTTGAAATTAAATTTA
1 TTTTAATTTGAAATTAAATTTA
* *
38702963 TTTTAATTTTAAATTCAATTT
1 TTTTAATTTGAAATTAAATTT
38702984 TAAAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAATTTGAAATTAAATTTA
Found at i:38703003 original size:18 final size:17
Alignment explanation
Indices: 38702951--38703004 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
38702941 TTTTACTTTG
*
38702951 AAATTAAATTTATTTTA
1 AAATTAAATTTAATTTA
** *
38702968 ATTTTAAATTCAATTTTA
1 AAATTAAATTTAA-TTTA
38702986 AAATTAAATTTGAATTTA
1 AAATTAAATTT-AATTTA
38703004 A
1 A
38703005 CTTGAATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 9 0.32
18 17 0.61
19 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTAAATTTAATTTA
Found at i:38704961 original size:30 final size:29
Alignment explanation
Indices: 38704925--38705039 Score: 140
Period size: 30 Copynumber: 3.9 Consensus size: 29
38704915 AGTTGTCCAG
*
38704925 AAATTACATTTTGACCTCAAAACTTTTCTA
1 AAATTACATTTTGACCCCAAAAC-TTTCTA
38704955 AAATTACATTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTCT-A
* * * *
38704985 AAATTATACTTTGACCCCGAAACTTTCAA
1 AAATTACATTTTGACCCCAAAACTTTCTA
* *
38705014 AAATTACCATTTTTACCCCCAAACTT
1 AAATTA-CATTTTGACCCCAAAACTT
38705040 CCCTAAATCC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.16
30 62 0.84
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATTACATTTTGACCCCAAAACTTTCTA
Found at i:38705075 original size:60 final size:57
Alignment explanation
Indices: 38705011--38705208 Score: 200
Period size: 59 Copynumber: 3.4 Consensus size: 57
38705001 CCGAAACTTT
* * *
38705011 CAAAAATTACCATTTTTACCCCCAAACTTCCCTAAATCCCATTTTTACCCCCGATTTCAC
1 CAAAAATTACCA-TTTTACCCCCAAACTTTCC-AAATTCCATTTTTA-CCTCGATTTCAC
* * * * * * * **
38705071 CAAAACTTACCGTTTTGCCTCCAAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTT-ACCTCGATTTCAC
* *
38705130 CAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCTCGATTTCA-
1 CAAAAATTACCATTTTA-CCCCCAAACTTTCCAAATTCCATTTTTA-CCTCGATTTCAC
38705188 CAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTACCCC
38705209 TAAAAACCCA
Statistics
Matches: 110, Mismatches: 25, Indels: 9
0.76 0.17 0.06
Matches are distributed among these distances:
57 3 0.03
58 17 0.15
59 67 0.61
60 23 0.21
ACGTcount: A:0.29, C:0.30, G:0.04, T:0.37
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTCCATTTTTACCTCGATTTCAC
Found at i:38709933 original size:47 final size:47
Alignment explanation
Indices: 38709878--38709971 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
38709868 ATCATTTCTG
38709878 GGTTTGGGTGGGAGATCTATAAATTTTATTCCTATAATTGGTTATTT
1 GGTTTGGGTGGGAGATCTATAAATTTTATTCCTATAATTGGTTATTT
38709925 GGTTTGGGTGGGAGATCTATAAATTTTATTCCTATAATTGGTTATTT
1 GGTTTGGGTGGGAGATCTATAAATTTTATTCCTATAATTGGTTATTT
38709972 TTTTTCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.47
Consensus pattern (47 bp):
GGTTTGGGTGGGAGATCTATAAATTTTATTCCTATAATTGGTTATTT
Found at i:38712038 original size:24 final size:24
Alignment explanation
Indices: 38712022--38712072 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
38712012 AGTTTGACTT
38712022 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
38712046 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
38712070 AAA
1 AAA
38712073 TATTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:38713736 original size:9 final size:9
Alignment explanation
Indices: 38713722--38713764 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
38713712 ATTTTTAAAA
*
38713722 ATTAAAATC
1 ATTAAAATT
38713731 ATTAAAATT
1 ATTAAAATT
*
38713740 ATTAAAA-A
1 ATTAAAATT
38713748 ATTAAAAATT
1 ATT-AAAATT
38713758 ATTAAAA
1 ATTAAAA
38713765 AATTATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.10
9 23 0.79
10 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAAATT
Found at i:38713745 original size:18 final size:18
Alignment explanation
Indices: 38713734--38713769 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
38713724 TAAAATCATT
38713734 AAAATTATTAAAAAATTA
1 AAAATTATTAAAAAATTA
38713752 AAAATTATTAAAAAATTA
1 AAAATTATTAAAAAATTA
38713770 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTATTAAAAAATTA
Found at i:38713750 original size:11 final size:10
Alignment explanation
Indices: 38713725--38713770 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 10
38713715 TTTAAAAATT
*
38713725 AAAATCATT-
1 AAAATTATTA
38713734 AAAATTATTA
1 AAAATTATTA
38713744 AAAA--ATTA
1 AAAATTATTA
38713752 AAAATTATTAA
1 AAAATTATT-A
38713763 AAAATTAT
1 AAAATTAT
38713771 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.25
9 8 0.25
10 7 0.22
11 9 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTATTA
Found at i:38713753 original size:17 final size:17
Alignment explanation
Indices: 38713731--38713774 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
38713721 AATTAAAATC
38713731 ATTAAAATTATTAAAAA
1 ATTAAAATTATTAAAAA
38713748 ATTAAAAATTATTAAAAA
1 ATT-AAAATTATTAAAAA
*
38713766 ATTATAATT
1 ATTAAAATT
38713775 TTTTTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAAATTATTAAAAA
Found at i:38713769 original size:26 final size:26
Alignment explanation
Indices: 38713718--38713769 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
38713708 AACTATTTTT
*
38713718 AAAAATTAAAATCATTAAAATTATTA
1 AAAAATTAAAATCATTAAAATAATTA
*
38713744 AAAAATTAAAAATTATTAAAA-AATTA
1 AAAAATT-AAAATCATTAAAATAATTA
38713770 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAATTAAAATCATTAAAATAATTA
Found at i:38714001 original size:21 final size:21
Alignment explanation
Indices: 38713962--38714001 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38713952 TAAAAAATTA
*
38713962 AAACAATTTTTTATAAAGTCG
1 AAACAATTTATTATAAAGTCG
38713983 AAACAA-TTATTATAGAAGT
1 AAACAATTTATTATA-AAGT
38714002 ACATCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
AAACAATTTATTATAAAGTCG
Found at i:38717991 original size:45 final size:45
Alignment explanation
Indices: 38717927--38718019 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
38717917 CAAAACCTTA
38717927 AAAAAATAAGAGAGGGTGAGAATTAATTGCTACCTCCACCACCTG
1 AAAAAATAAGAGAGGGTGAGAATTAATTGCTACCTCCACCACCTG
38717972 AAAAAATAAGAGAGGGTGAGAATTAATTGCTACCTCCACCACCTG
1 AAAAAATAAGAGAGGGTGAGAATTAATTGCTACCTCCACCACCTG
38718017 AAA
1 AAA
38718020 TCTTTGATGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (45 bp):
AAAAAATAAGAGAGGGTGAGAATTAATTGCTACCTCCACCACCTG
Found at i:38718241 original size:35 final size:34
Alignment explanation
Indices: 38718173--38718239 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
38718163 TAACAATTAA
*
38718173 TTGAGGTTCAAAAAAGGATTCTCATCTTCAAAATT
1 TTGAGGTTCAAAAAA-GATTCTCACCTTCAAAATT
38718208 TTGAGGTT-AAAAAA-ATGTCTTCACCTTCAAAA
1 TTGAGGTTCAAAAAAGAT-TC-TCACCTTCAAAA
38718240 ATCTCAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 2 0.07
33 2 0.07
34 17 0.59
35 8 0.28
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (34 bp):
TTGAGGTTCAAAAAAGATTCTCACCTTCAAAATT
Found at i:38718513 original size:3 final size:3
Alignment explanation
Indices: 38718505--38718548 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
38718495 ACATCTCCAT
* *
38718505 TTC TTC TTC TTC TTC TTT TTC TTC -TC TTT TTC -TC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
38718549 ATTACACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:38719741 original size:21 final size:21
Alignment explanation
Indices: 38719717--38719766 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
38719707 TTTAAGTTCC
38719717 AAATTTTAAG-TTTAGAGATTA
1 AAATTTTAAGATTTA-AGATTA
*
38719738 AAATTTTAAGATTTAAGATTT
1 AAATTTTAAGATTTAAGATTA
*
38719759 AAGTTTTA
1 AAATTTTA
38719767 TGTATTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (21 bp):
AAATTTTAAGATTTAAGATTA
Found at i:38720741 original size:23 final size:24
Alignment explanation
Indices: 38720685--38720752 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
38720675 AATTGGATGA
38720685 AATAGTAAAAATATATAATATTTTC
1 AATA-TAAAAATATATAATATTTTC
* *
38720710 AATAAAAAAATATAT-ATATTTTT
1 AATATAAAAATATATAATATTTTC
* *
38720733 ACTTTAAAAATA-ATAATATT
1 AATATAAAAATATATAATATT
38720753 AAAAAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.05
23 21 0.57
24 10 0.27
25 4 0.11
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (24 bp):
AATATAAAAATATATAATATTTTC
Found at i:38727659 original size:13 final size:13
Alignment explanation
Indices: 38727641--38727666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38727631 TTAGCATTGC
38727641 TTTTAAAAAGTGT
1 TTTTAAAAAGTGT
38727654 TTTTAAAAAGTGT
1 TTTTAAAAAGTGT
38727667 GGTGAAAAAG
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTTAAAAAGTGT
Found at i:38729657 original size:41 final size:38
Alignment explanation
Indices: 38729557--38729660 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
38729547 TTCGAAGCAA
*
38729557 TAAAGTGACACCCAGTGTCTCATCG-ACCTAACCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAACCGAAG
* * ** ** * *
38729594 TGAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAACCGAAG
38729632 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
38729661 CTCAAGGTTG
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 20 0.40
38 11 0.22
40 1 0.02
41 18 0.36
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAACCGAAG
Found at i:38740561 original size:23 final size:23
Alignment explanation
Indices: 38740511--38740555 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
38740501 TGTCCGAAAT
38740511 ATTGCGACCTGCAATGAAACCAG
1 ATTGCGACCTGCAATGAAACCAG
38740534 ATTGCGACCTGCAATGAAACCA
1 ATTGCGACCTGCAATGAAACCA
38740556 ACTTGCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.18
Consensus pattern (23 bp):
ATTGCGACCTGCAATGAAACCAG
Found at i:38745371 original size:31 final size:31
Alignment explanation
Indices: 38745312--38745372 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
38745302 AGCCTAGTGA
* *
38745312 TTTAAATAAAAACTTTTGAATAATTCAATGG
1 TTTAAATAAAAACTTTCGAATAACTCAATGG
* *
38745343 TTTAAATGAAAACTTTCGAATAGCTCAATG
1 TTTAAATAAAAACTTTCGAATAACTCAATG
38745373 ATCATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (31 bp):
TTTAAATAAAAACTTTCGAATAACTCAATGG
Found at i:38745910 original size:59 final size:61
Alignment explanation
Indices: 38745750--38745929 Score: 144
Period size: 59 Copynumber: 3.0 Consensus size: 61
38745740 ATTTTAATAT
* * ** * * * *
38745750 TTTTTCTTAATTTGGTA-TCTAAATATTTTTTGTGGCTCAATTCGATGCTTTAACTTGACAAA
1 TTTTTCTTAATTTGATACT-TAAGT-TTTTTTCAGGTTCAATTTGATACTTAAACTTGACAAA
* * *
38745812 TTTTTC-TAATTTTATAAC-TAAGCTTTTTTTCA--TTTAATTTGATACTTAAATTTGAC-AA
1 TTTTTCTTAATTTGAT-ACTTAAG-TTTTTTTCAGGTTCAATTTGATACTTAAACTTGACAAA
*
38745870 TTTTTCTTAATTTGATACTTAAGTTTTTTT-AGGTTCAATTTG-TA-TCTAAACTTGTCAAA
1 TTTTTCTTAATTTGATACTTAAGTTTTTTTCAGGTTCAATTTGATACT-TAAACTTGACAAA
38745929 T
1 T
38745930 GATTTACAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
57 2 0.02
58 27 0.29
59 41 0.44
61 16 0.17
62 8 0.09
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (61 bp):
TTTTTCTTAATTTGATACTTAAGTTTTTTTCAGGTTCAATTTGATACTTAAACTTGACAAA
Found at i:38752858 original size:224 final size:224
Alignment explanation
Indices: 38752468--38752909 Score: 760
Period size: 224 Copynumber: 2.0 Consensus size: 224
38752458 GAAAAGTAAT
* *
38752468 TATATGAAAATTAAGAATGTATATTTATGAAAATATCACGTAATTAATGTAGAAATAAGTTTTAT
1 TATATGAAAATTAAGAATGTATATCTATGAAAATATCACGTAATTAATGTAGAAATAAGTTTCAT
* *
38752533 GAGAACTAAATTGTACACAATTAGCGCTTAAACCATCCAAAAACAAAAACAGTTGTTGAATAATT
66 GAGAACTAAATTGTACACAATTAACGCTTAAACCAACCAAAAACAAAAACAGTTGTTGAATAATT
38752598 ATTAGAAGTCATTAGTACCGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAA-AATATTGAT
131 ATTAGAAGTCATTAGTACCGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAATAA-ATTGAT
*
38752662 CAAATAAAAGAGGGGCCGACTAGAAATAGA
195 CAAATAAAAGAGAGGCCGACTAGAAATAGA
*
38752692 TATATGAAAATTAAGAATGTATATCTATGAAAATTTCACGTAATTAATGTAGAAATAAGTTTCAT
1 TATATGAAAATTAAGAATGTATATCTATGAAAATATCACGTAATTAATGTAGAAATAAGTTTCAT
* * *
38752757 GAGAACTAAATTGTATACAATTAACGCTTAAACCAACCAAAAACAAAAATAGTTGTTGGATAATT
66 GAGAACTAAATTGTACACAATTAACGCTTAAACCAACCAAAAACAAAAACAGTTGTTGAATAATT
** *
38752822 ATTAGAAGTCATTAGTAGTGAGTGCATGATTTGAAAGTGTTCAATTATTTATAAATAAATTGATC
131 ATTAGAAGTCATTAGTACCGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAATAAATTGATC
38752887 AAATAAAAGAGAGGCCGACTAGA
196 AAATAAAAGAGAGGCCGACTAGA
38752910 CTGAAGAAAA
Statistics
Matches: 205, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
224 203 0.99
225 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.31
Consensus pattern (224 bp):
TATATGAAAATTAAGAATGTATATCTATGAAAATATCACGTAATTAATGTAGAAATAAGTTTCAT
GAGAACTAAATTGTACACAATTAACGCTTAAACCAACCAAAAACAAAAACAGTTGTTGAATAATT
ATTAGAAGTCATTAGTACCGAGTGCATGATTTGAAAGTGTTCAATCATTTATAAATAAATTGATC
AAATAAAAGAGAGGCCGACTAGAAATAGA
Found at i:38755458 original size:220 final size:221
Alignment explanation
Indices: 38755057--38755479 Score: 652
Period size: 220 Copynumber: 1.9 Consensus size: 221
38755047 TGAGTAGGTG
* * * *
38755057 GGAGTGTGATGCCTATCCTACATCAGATGCGAGTGTGATTGTTAAAGATCCATATAAAGGTCGAA
1 GGAGTGTGATGCCCATCCTACATCAGATGCGAGTGTGATTATTAAAGATCCATAAAAAGGTCAAA
*
38755122 GTCCATCATTACTAGCAACAGGAGCATAAGCTTTTTACATCACATGGTTTTGGTCCATAAAAGTC
66 GTCCATCATTACTAGCAACAGGAGCATAAGCCTTTTACATCACATGGTTTTGGTCCATAAAAGTC
* * *
38755187 ACTGGACTAGTGGTGCTTTGAGTGAGATGAACAATATTGAAACAATTTCCCTGAGCAATAGGCTT
131 ACTGGACTAGGGGTGCTTTGAGTGAGATGAACAATACTGAAACAATTTCCCTGAGCAATAGCCTT
*
38755252 TTTTGCACTGGGCATCACACTGGGTA
196 TTCTGCACTGGGCATCACACTGGGTA
* *
38755278 GGAGTGTGATGCCCA-CACTACTTCAGATGTGAGTGTGATTATT-AAGATCCATAAAAAGGTCAA
1 GGAGTGTGATGCCCATC-CTACATCAGATGCGAGTGTGATTATTAAAGATCCATAAAAAGGTCAA
* *
38755341 AGTCCATCATTACTAGCAACTGGAGCATAAGCCTTTTACATCACGTGGTTTTGGTCCATAAAAGT
65 AGTCCATCATTACTAGCAACAGGAGCATAAGCCTTTTACATCACATGGTTTTGGTCCATAAAAGT
* * * ** *
38755406 CAGTGGACTAGGGGTGCTTTGAGTGCGATGAACCATACTGAAACGGTTTCCCTGAGCAGTAGCCT
130 CACTGGACTAGGGGTGCTTTGAGTGAGATGAACAATACTGAAACAATTTCCCTGAGCAATAGCCT
38755471 TTTCTGCAC
195 TTTCTGCAC
38755480 ACATCACCCC
Statistics
Matches: 182, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
220 145 0.80
221 37 0.20
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (221 bp):
GGAGTGTGATGCCCATCCTACATCAGATGCGAGTGTGATTATTAAAGATCCATAAAAAGGTCAAA
GTCCATCATTACTAGCAACAGGAGCATAAGCCTTTTACATCACATGGTTTTGGTCCATAAAAGTC
ACTGGACTAGGGGTGCTTTGAGTGAGATGAACAATACTGAAACAATTTCCCTGAGCAATAGCCTT
TTCTGCACTGGGCATCACACTGGGTA
Found at i:38779133 original size:10 final size:9
Alignment explanation
Indices: 38779094--38779289 Score: 80
Period size: 9 Copynumber: 21.0 Consensus size: 9
38779084 CTTGTGGCAA
*
38779094 AAAAATGAT
1 AAAAATTAT
*
38779103 AAAAAATA-
1 AAAAATTAT
*
38779111 AAAAATAAT
1 AAAAATTAT
*
38779120 AAAAGTTAT
1 AAAAATTAT
38779129 AAAAATTAT
1 AAAAATTAT
* * *
38779138 TAAATTTAA
1 AAAAATTAT
*
38779147 AAAAATATTT
1 AAAAAT-TAT
**
38779157 AAATTTTATT
1 AAAAATTA-T
38779167 AAAAATTA-
1 AAAAATTAT
38779175 AAAAA-TAT
1 AAAAATTAT
38779183 ATAAAATATAT
1 A-AAAAT-TAT
* *
38779194 AGAAATATAG
1 AAAAAT-TAT
38779204 AATAAATTAT
1 AA-AAATTAT
*
38779214 -AAAATTTT
1 AAAAATTAT
* *
38779222 ATAAAGTCAT
1 A-AAAATTAT
38779232 AAGAAAATTAT
1 -A-AAAATTAT
38779243 AGAAAATGTA-
1 A-AAAAT-TAT
38779253 AAGAAA-TAT
1 AA-AAATTAT
**
38779262 AAAAATCGT
1 AAAAATTAT
38779271 AAAAATTTAT
1 AAAAA-TTAT
38779281 AAAAATTAT
1 AAAAATTAT
38779290 TGTACTAAAA
Statistics
Matches: 137, Mismatches: 34, Indels: 32
0.67 0.17 0.16
Matches are distributed among these distances:
7 2 0.01
8 23 0.17
9 50 0.36
10 45 0.33
11 17 0.12
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:38779491 original size:20 final size:20
Alignment explanation
Indices: 38779468--38779536 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
38779458 TTTTGATGCA
38779468 TTTTATAAATTTTTTATAAT
1 TTTTATAAATTTTTTATAAT
**
38779488 TTTTATAAAAATTTTATAAT
1 TTTTATAAATTTTTTATAAT
**
38779508 TTTT-TATAATTTTTTATGGT
1 TTTTATA-AATTTTTTATAAT
38779528 TTTTATAAA
1 TTTTATAAA
38779537 AAAAAATCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.05
20 37 0.90
21 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATAAATTTTTTATAAT
Found at i:38779531 original size:10 final size:10
Alignment explanation
Indices: 38779468--38779524 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
38779458 TTTTGATGCA
38779468 TTTTATAAATT
1 TTTTAT-AATT
38779479 TTTTATAA-T
1 TTTTATAATT
**
38779488 TTTTATAAAAA
1 TTTTAT-AATT
38779499 TTTTATAATT
1 TTTTATAATT
38779509 TTTTATAATT
1 TTTTATAATT
38779519 TTTTAT
1 TTTTAT
38779525 GGTTTTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 7 0.17
10 22 0.54
11 12 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:38779552 original size:40 final size:40
Alignment explanation
Indices: 38779468--38779573 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
38779458 TTTTGATGCA
***
38779468 TTTTATAAATTTTTTATAATTTTTATAAAAATTTTATAATT
1 TTTTAT-AATTTTTTATAATTTTTATAAAAAAAATATAATT
** *
38779509 TTTTATAATTTTTTATGGTTTTTATAAAAAAAAATCTAATT
1 TTTTATAATTTTTTATAATTTTTAT-AAAAAAAATATAATT
*
38779550 TTTAATAA-TTTTTAT-ATTTTTATA
1 TTTTATAATTTTTTATAATTTTTATA
38779574 TTTTTTTCAC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.02
39 7 0.12
40 24 0.43
41 24 0.43
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (40 bp):
TTTTATAATTTTTTATAATTTTTATAAAAAAAATATAATT
Found at i:38780158 original size:15 final size:16
Alignment explanation
Indices: 38780130--38780159 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38780120 AAGTTGTGAT
38780130 AATTATAGATTTAAAA
1 AATTATAGATTTAAAA
38780146 AATTATA-ATTTAAA
1 AATTATAGATTTAAA
38780160 GAAGTTGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AATTATAGATTTAAAA
Found at i:38780183 original size:41 final size:43
Alignment explanation
Indices: 38780120--38780201 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 43
38780110 AATAAAATGA
* * *
38780120 AAGTTGTGATAATTATAGATTT-AAAA-AATTATAATTTAAAG
1 AAGTTGTGATAATTAGACATTTAAAAATAATTAGAATTTAAAG
*
38780161 AAGTTGTGGTAATTAGACATTTAAAAATAATTAGAATTTAA
1 AAGTTGTGATAATTAGACATTTAAAAATAATTAGAATTTAA
38780202 GTTACAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 19 0.54
42 4 0.11
43 12 0.34
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (43 bp):
AAGTTGTGATAATTAGACATTTAAAAATAATTAGAATTTAAAG
Found at i:38787399 original size:18 final size:18
Alignment explanation
Indices: 38787361--38787402 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38787351 AACGATTAGT
** *
38787361 AGTTCGTCGTCGTGTCGG
1 AGTTCGTCGTCGCCTCAG
38787379 AGTTCGTCGTCGCCTCAG
1 AGTTCGTCGTCGCCTCAG
38787397 AGTTCG
1 AGTTCG
38787403 CCGTATGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.26, G:0.33, T:0.31
Consensus pattern (18 bp):
AGTTCGTCGTCGCCTCAG
Found at i:38806409 original size:216 final size:215
Alignment explanation
Indices: 38806068--38807110 Score: 1274
Period size: 216 Copynumber: 4.8 Consensus size: 215
38806058 TCTTCCACTG
* * * * * * *
38806068 CTAAGGCCATCTTAGATTCCATATTCAAAGTAATAC-CTTCAATTTTACCAATTCTCTCACCATT
1 CTAAAGCCATCTTAGACTCCGTATTCAAAATAGTACAC-TCAATTTTACCAATTCCCTCACCTTT
* * * * *
38806132 TTCCTCGGCACCACTATTTTCTTCCTCCTCCAGCTTAACACTGTGAGGAACTTCGCTTTTGGAAC
65 TTCCTCAGCACCAGTATTTTCTTCCTCTTCCAACTTAACACTGTG-GGAACTTCACTTTTGGAAC
* * * * *
38806197 TAAACTCTAAAGGAGCTAATTCAGTTCTAGTTTCACTTTCACTAGCAGGAGCTTCCAATGGAGGA
129 TGAACTCTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGA
**
38806262 GAAGCCTTTTCTAAATCAGGAA
194 GAAGCCTTTTCTGTATCAGGAA
* * * * **
38806284 CTAAAGCCAT-TGTAGACTCCATATTCGAAGTAGTACACTCAAATTTACCAATTCTTTCACCTTT
1 CTAAAGCCATCT-TAGACTCCGTATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTT
* * * *
38806348 TTCCTCAGCACTAGTATCTCCTTCCTCTTCCAACTTAACACTCTGGGAATCTTCACTTTTGGAAC
65 TTCCTCAGCACCAGTATTTTCTTCCTCTTCCAACTTAACACTGTGGGAA-CTTCACTTTTGGAAC
* * * * *
38806413 CGGACTCTAAAGAAGCTAATTCAGTTGTAATTTCACTTTCAATGGCAGAAGCTTCCAGTGGAGGA
129 TGAACTCTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGA
*
38806478 GAAGCCTTTTCTTTATCAGGAA
194 GAAGCCTTTTCTGTATCAGGAA
* * * *
38806500 CTAAAGCTATCTTAGACTCCGTATTCAAAACAGTATACTCAATTTTACCAATTCCCTCACCTTGT
1 CTAAAGCCATCTTAGACTCCGTATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTT
*
38806565 TCCTCAGCACCAGTATTTTCTTCCTCTTCCAACTTAACACACTG-GGGAACTTCACTTTTAGAAC
66 TCCTCAGCACCAGTATTTTCTTCCTCTTCCAACTT-A-ACACTGTGGGAACTTCACTTTTGGAAC
* * * * *
38806629 TGGACTCTGAAGGAGCTAATTCAGTAGTAATTTCACTTTCAATAGCAAAAGCTTCCAGTGGAGGA
129 TGAACTCTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGA
38806694 GAAGCCTTTTCTGTATCAGGAA
194 GAAGCCTTTTCTGTATCAGGAA
* *
38806716 CTAAAGCCATCTTAGACTCTGTATTCGAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTT
1 CTAAAGCCATCTTAGACTCCGTATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTT
*
38806781 TCCTCAGCACCAGCATTTTCTTCCTCTTCCAACTTAACACTGTGGGGAACTTCACTTTTGGAACT
66 TCCTCAGCACCAGTATTTTCTTCCTCTTCCAACTTAACACTGT-GGGAACTTCACTTTTGGAACT
* * * * *
38806846 GAACTCTGAAGGAGCTAATTCAGTTGTAATTGCACTTTCAATAGCAGAAACTT-CAAGTGGAAGC
130 GAACTCTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAA-TGGAGGA
* *
38806910 GGAGCCTTTTCTGTATCAAGAA
194 GAAGCCTTTTCTGTATCAGGAA
* *
38806932 CTAAAGCCA---TAGACTCCGTATTCAAAATAGTACACTCAGTTTTACC-ATATCCCTCACCATT
1 CTAAAGCCATCTTAGACTCCGTATTCAAAATAGTACACTCAATTTTACCAAT-TCCCTCACCTTT
** * * ** ***
38806993 TTCCTCAGCACCAGCGTTGTCTTCTTCTTCCAACTTAACACTGTGGGGAACGCCACTTTCCAAAC
65 TTCCTCAGCACCAGTATTTTCTTCCTCTTCCAACTTAACACTGT-GGGAACTTCACTTTTGGAAC
* * * * * * * *
38807058 CGGACTCTGAAGTAGCCAATTCAGTTGTCATTTCACTTCCAATACCAGAAGCT
129 TGAACTCTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCT
38807111 CCCAGTTCCT
Statistics
Matches: 728, Mismatches: 89, Indels: 23
0.87 0.11 0.03
Matches are distributed among these distances:
212 2 0.00
213 146 0.20
214 6 0.01
215 8 0.01
216 553 0.76
217 8 0.01
218 5 0.01
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (215 bp):
CTAAAGCCATCTTAGACTCCGTATTCAAAATAGTACACTCAATTTTACCAATTCCCTCACCTTTT
TCCTCAGCACCAGTATTTTCTTCCTCTTCCAACTTAACACTGTGGGAACTTCACTTTTGGAACTG
AACTCTAAAGGAGCTAATTCAGTTGTAATTTCACTTTCAATAGCAGAAGCTTCCAATGGAGGAGA
AGCCTTTTCTGTATCAGGAA
Found at i:38810862 original size:29 final size:29
Alignment explanation
Indices: 38810829--38810936 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 29
38810819 TTTACCTCAG
* *
38810829 GTTACATATTAGTTACTTATGTTTGCAAT
1 GTTACATTTTAGTCACTTATGTTTGCAAT
* **
38810858 GTTACGTTTTAGTCACTTACATTAT-C-AT
1 GTTACATTTTAGTCACTTATGTT-TGCAAT
38810886 GTTGTAACATTTTAGTCACTTATGTTTGCAAT
1 G-T-T-ACATTTTAGTCACTTATGTTTGCAAT
*
38810918 GTTACGTTTTAGTCACTTA
1 GTTACATTTTAGTCACTTA
38810937 CGTTATCATG
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
28 3 0.05
29 35 0.55
30 4 0.06
31 19 0.30
32 3 0.05
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTATGTTTGCAAT
Found at i:38810899 original size:31 final size:31
Alignment explanation
Indices: 38810864--38810965 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 31
38810854 CAATGTTACG
*
38810864 TTTTAGTCACTTACATTATCATGTTGTAACA
1 TTTTAGTCACTTACGTTATCATGTTGTAACA
* *
38810895 TTTTAGTCACTTATGTT-TGCAATG-T-T-ACG
1 TTTTAGTCACTTACGTTAT-C-ATGTTGTAACA
*
38810924 TTTTAGTCACTTACGTTATCATGTTGCAACA
1 TTTTAGTCACTTACGTTATCATGTTGTAACA
38810955 TTTTAGTCACT
1 TTTTAGTCACT
38810966 GAGCCGTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
28 3 0.05
29 20 0.34
30 3 0.05
31 30 0.51
32 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.46
Consensus pattern (31 bp):
TTTTAGTCACTTACGTTATCATGTTGTAACA
Found at i:38810907 original size:60 final size:60
Alignment explanation
Indices: 38810832--38810965 Score: 232
Period size: 60 Copynumber: 2.2 Consensus size: 60
38810822 ACCTCAGGTT
* * *
38810832 ACATATTAGTTACTTATGTTTGCAATGTTACGTTTTAGTCACTTACATTATCATGTTGTA
1 ACATTTTAGTCACTTATGTTTGCAATGTTACGTTTTAGTCACTTACATTATCATGTTGCA
*
38810892 ACATTTTAGTCACTTATGTTTGCAATGTTACGTTTTAGTCACTTACGTTATCATGTTGCA
1 ACATTTTAGTCACTTATGTTTGCAATGTTACGTTTTAGTCACTTACATTATCATGTTGCA
38810952 ACATTTTAGTCACT
1 ACATTTTAGTCACT
38810966 GAGCCGTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (60 bp):
ACATTTTAGTCACTTATGTTTGCAATGTTACGTTTTAGTCACTTACATTATCATGTTGCA
Found at i:38811379 original size:25 final size:25
Alignment explanation
Indices: 38811362--38811408 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
38811352 AAATATAATG
38811362 GAAAAT-AAAGAAAAAAAATTAAAA
1 GAAAATAAAAGAAAAAAAATTAAAA
*
38811386 GAACATAAAAG-AAAAAAATTAAA
1 GAAAATAAAAGAAAAAAAATTAAA
38811409 TTGCTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (25 bp):
GAAAATAAAAGAAAAAAAATTAAAA
Found at i:38830146 original size:15 final size:15
Alignment explanation
Indices: 38830126--38830155 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38830116 CAACTGGAAC
38830126 AGTATTAAAATTCTG
1 AGTATTAAAATTCTG
38830141 AGTATTAAAATTCTG
1 AGTATTAAAATTCTG
38830156 TGTTGGAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
AGTATTAAAATTCTG
Found at i:38831498 original size:62 final size:62
Alignment explanation
Indices: 38831401--38831549 Score: 246
Period size: 62 Copynumber: 2.4 Consensus size: 62
38831391 CTCTAACAGT
*
38831401 AAGGCAACCAATCAATGTTAGGGTTCGACTATGGCAACATATGGAATGTTAGGGCTCACATG
1 AAGGCAACCAATTAATGTTAGGGTTCGACTATGGCAACATATGGAATGTTAGGGCTCACATG
* *
38831463 AAGGCAACCAATTAATGTTAGGGTTCGACTATGGCAACCTATGGAATGTTAGGGCTCACGTG
1 AAGGCAACCAATTAATGTTAGGGTTCGACTATGGCAACATATGGAATGTTAGGGCTCACATG
* *
38831525 AAGGCAGCCAATTAAT-TCAGGGTTC
1 AAGGCAACCAATTAATGTTAGGGTTC
38831550 ACATAAGGTT
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 8 0.10
62 74 0.90
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (62 bp):
AAGGCAACCAATTAATGTTAGGGTTCGACTATGGCAACATATGGAATGTTAGGGCTCACATG
Found at i:38831501 original size:30 final size:31
Alignment explanation
Indices: 38831403--38831516 Score: 128
Period size: 31 Copynumber: 3.7 Consensus size: 31
38831393 CTAACAGTAA
*
38831403 GGCAACCAAT-CAATGTTAGGGTTCGACTAT
1 GGCAACCAATGGAATGTTAGGGTTCGACTAT
* *
38831433 GGCAA-CATATGGAATGTTAGGGCTC-ACATGAA
1 GGCAACCA-ATGGAATGTTAGGGTTCGAC-T-AT
*
38831465 GGCAACCAAT-TAATGTTAGGGTTCGACTAT
1 GGCAACCAATGGAATGTTAGGGTTCGACTAT
*
38831495 GGCAACCTATGGAATGTTAGGG
1 GGCAACCAATGGAATGTTAGGG
38831517 CTCACGTGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.03
30 19 0.28
31 36 0.52
32 10 0.14
33 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (31 bp):
GGCAACCAATGGAATGTTAGGGTTCGACTAT
Found at i:38832957 original size:23 final size:25
Alignment explanation
Indices: 38832916--38832971 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
38832906 TTTATAAAAA
* *
38832916 CATTGTTTTAATTCATTT-AATTTTT
1 CATTTTTTTAATT-ATTTAAATTTGT
38832941 CATTTTTTTAATT-TTTAAATTTGT
1 CATTTTTTTAATTATTTAAATTTGT
38832965 -ATTTTTT
1 CATTTTTT
38832972 ATCAAATCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 10 0.36
24 6 0.21
25 12 0.43
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (25 bp):
CATTTTTTTAATTATTTAAATTTGT
Found at i:38836574 original size:18 final size:18
Alignment explanation
Indices: 38836540--38836574 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38836530 TGAAGTTTAT
* *
38836540 ATTTAAAATCTTTAAAGG
1 ATTTAAAATATTGAAAGG
38836558 ATTTAAAATATTGAAAG
1 ATTTAAAATATTGAAAG
38836575 CATATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (18 bp):
ATTTAAAATATTGAAAGG
Found at i:38844356 original size:6 final size:6
Alignment explanation
Indices: 38844322--38844389 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
38844312 TAATAGGGAT
* * * * *
38844322 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA CTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
38844369 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
38844390 TGATCACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 44 0.86
7 3 0.06
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTCAA
Found at i:38844364 original size:18 final size:18
Alignment explanation
Indices: 38844341--38844389 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
38844331 ACAATTCATA
38844341 TCACTTTCAATTTCAAC-T
1 TCACTTTCAATTTC-ACTT
*
38844359 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCACTT
38844377 TCACTTTCAATTT
1 TCACTTTCAATTT
38844390 TGATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTTCACTT
Found at i:38844366 original size:12 final size:13
Alignment explanation
Indices: 38844343--38844385 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
38844333 AATTCATATC
*
38844343 ACTTTCAATTTCA
1 ACTTTCACTTTCA
38844356 AC-TTCACTTTC-
1 ACTTTCACTTTCA
38844367 ACTTTCACTTTC-
1 ACTTTCACTTTCA
38844379 ACTTTCA
1 ACTTTCA
38844386 ATTTTGATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 2 0.07
12 24 0.86
13 2 0.07
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:38849631 original size:31 final size:29
Alignment explanation
Indices: 38849577--38849648 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
38849567 AATATATGTG
* *
38849577 AATTTTA-TTTCTCTACTTTAATTTATT-T
1 AATTTTAGTTTTTCTACTTTAATTT-TTAA
*
38849605 ATTTTTAGTTTTTCTACTTTTAAATTTTTAA
1 AATTTTAGTTTTTCTAC-TTT-AATTTTTAA
38849636 AATTTTAGTTTTT
1 AATTTTAGTTTTT
38849649 ATCAAACTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.17
29 8 0.22
30 5 0.14
31 17 0.47
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (29 bp):
AATTTTAGTTTTTCTACTTTAATTTTTAA
Found at i:38852285 original size:31 final size:31
Alignment explanation
Indices: 38852247--38852307 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
38852237 ATGTGTTTAA
*
38852247 TTGAATCAAAATGAAAATTTCATGTATATAT
1 TTGAATCAAAATGAAAATTTCATGCATATAT
* *
38852278 TTGAATCATAATTAAAATTTCATGCATATA
1 TTGAATCAAAATGAAAATTTCATGCATATA
38852308 ATTACACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (31 bp):
TTGAATCAAAATGAAAATTTCATGCATATAT
Found at i:38860507 original size:16 final size:15
Alignment explanation
Indices: 38860481--38860512 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
38860471 GGATAAATAT
38860481 ATAAATAATAATAAA
1 ATAAATAATAATAAA
38860496 ATAAATTAATAATAAA
1 ATAAA-TAATAATAAA
38860512 A
1 A
38860513 CTTGTTGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAATAATAAA
Found at i:38865611 original size:2 final size:2
Alignment explanation
Indices: 38865604--38865628 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38865594 CTAAACAGAA
38865604 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
38865629 GAGGTAGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:38867898 original size:2 final size:2
Alignment explanation
Indices: 38867891--38867915 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38867881 ATTATAGTAA
38867891 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38867916 CACAAATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38872457 original size:6 final size:6
Alignment explanation
Indices: 38872443--38872473 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
38872433 AAACAGCACG
*
38872443 AACAGC AACATC AACATC AACATC AACATC A
1 AACATC AACATC AACATC AACATC AACATC A
38872474 TGTCCATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.52, C:0.32, G:0.03, T:0.13
Consensus pattern (6 bp):
AACATC
Found at i:38875959 original size:23 final size:24
Alignment explanation
Indices: 38875907--38875961 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
38875897 ATAATGTTTG
* * *
38875907 ATAATAATTATATATAAATTACAA
1 ATAAAAATTATACATAAATAACAA
*
38875931 AT-AAAATTATACATAAA-AACAT
1 ATAAAAATTATACATAAATAACAA
38875953 ATAAAAATT
1 ATAAAAATT
38875962 CATTCGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 19 0.73
24 2 0.08
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAAAATTATACATAAATAACAA
Found at i:38877847 original size:77 final size:76
Alignment explanation
Indices: 38877717--38877867 Score: 203
Period size: 77 Copynumber: 2.0 Consensus size: 76
38877707 CATTTTAAAT
* * * * * *
38877717 ACATTTCACTTAAATTTGAACTACTAATTTGTGCGCAAGTTAAAGGTTGGACTAGTACTAGAGCT
1 ACATTTCACTTAAAATTGAACTACTAATTTGTGCACAAATTAAAGGTTAGACTAGGACTAGAACT
38877782 TCATCTATACA
66 TCATCTATACA
* * *
38877793 ACATTTCACTTTAAAATTGAACTAGTAATTTGTGCATAAATTAATGGTTAGACTAGGACTAGAAC
1 ACATTTCAC-TTAAAATTGAACTACTAATTTGTGCACAAATTAAAGGTTAGACTAGGACTAGAAC
*
38877858 TTTATCTATA
65 TTCATCTATA
38877868 TGATTAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
76 9 0.14
77 55 0.86
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (76 bp):
ACATTTCACTTAAAATTGAACTACTAATTTGTGCACAAATTAAAGGTTAGACTAGGACTAGAACT
TCATCTATACA
Found at i:38878899 original size:18 final size:18
Alignment explanation
Indices: 38878872--38878916 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
38878862 TAGTTCAAGG
*
38878872 TTTAACTAATTTAAAATT-
1 TTTAATTAA-TTAAAATTA
*
38878890 TTTAATTAATTAAATTTA
1 TTTAATTAATTAAAATTA
38878908 TTTAATTAA
1 TTTAATTAA
38878917 AAATCTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATTAATTAAAATTA
Found at i:38888810 original size:2 final size:2
Alignment explanation
Indices: 38888805--38888835 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38888795 GAATATATAA
38888805 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38888836 AGTTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38897548 original size:10 final size:9
Alignment explanation
Indices: 38897521--38897547 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38897511 AATTTAAGAT
38897521 TTTAAAAAA
1 TTTAAAAAA
38897530 TTTAAAAAA
1 TTTAAAAAA
38897539 TTTAAAAAA
1 TTTAAAAAA
38897548 AAAAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:38903605 original size:36 final size:36
Alignment explanation
Indices: 38903546--38903615 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
38903536 GGCCAACACC
*
38903546 AAAAAAAATTGAAATTTTCTTCTCGAGAATAGGGGT
1 AAAAAAAATTGAAATTTTCTTCTCGAGAAAAGGGGT
* * *
38903582 AAAAAAAATTGGATTTTTTTTCTCGAGAAAAGGG
1 AAAAAAAATTGAAATTTTCTTCTCGAGAAAAGGG
38903616 AGTGTCGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (36 bp):
AAAAAAAATTGAAATTTTCTTCTCGAGAAAAGGGGT
Found at i:38903682 original size:61 final size:61
Alignment explanation
Indices: 38903582--38903724 Score: 189
Period size: 61 Copynumber: 2.3 Consensus size: 61
38903572 GAATAGGGGT
* ** * *
38903582 AAAAAAAATTGGATTTTTTTTCTCGAGAAAAGGGAGTGTCGGTCATTTGAT-GAACAACACC
1 AAAAAAAATTGAATTTTTTTTCTCGAGAAAAGGGAGTGTCAATCATTTAATAG-ACAACACA
* * * *
38903643 TAAAAAAATTTAATTTTTTTTCTCGAGAAAAGGGGGTGTCAATCATTTAATAGCCAACACA
1 AAAAAAAATTGAATTTTTTTTCTCGAGAAAAGGGAGTGTCAATCATTTAATAGACAACACA
38903704 AAAAAAAATTGAATTTTTTTT
1 AAAAAAAATTGAATTTTTTTT
38903725 TGAAACAGGG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
61 69 0.99
62 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (61 bp):
AAAAAAAATTGAATTTTTTTTCTCGAGAAAAGGGAGTGTCAATCATTTAATAGACAACACA
Found at i:38905069 original size:26 final size:26
Alignment explanation
Indices: 38905037--38905090 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
38905027 TTTAAATAAA
*
38905037 TAGTTAATAGAATCAGTTGATCAAAT
1 TAGTTAATAGAATCAATTGATCAAAT
*
38905063 TAGTTAATAGAATCAATTGGTCAAAT
1 TAGTTAATAGAATCAATTGATCAAAT
38905089 TA
1 TA
38905091 AATTATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (26 bp):
TAGTTAATAGAATCAATTGATCAAAT
Found at i:38909905 original size:29 final size:27
Alignment explanation
Indices: 38909842--38909905 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
38909832 CAGTTGAATC
* **
38909842 TAAATTTTTAAATAAAAAATAATTAATT
1 TAAATTTGT-AATAAAAAATAATTAAAA
38909870 TAAATTTGTAATAAAAAATAAGATTAAAA
1 TAAATTTGTAATAAAAAAT-A-ATTAAAA
*
38909899 TATATTT
1 TAAATTT
38909906 TAACTTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 10 0.33
28 9 0.30
29 11 0.37
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAATTTGTAATAAAAAATAATTAAAA
Found at i:38916779 original size:16 final size:15
Alignment explanation
Indices: 38916752--38916781 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
38916742 ATTACCAGTT
38916752 ATGATGTTCTAATTG
1 ATGATGTTCTAATTG
38916767 ATGATGATTCTAATT
1 ATGATG-TTCTAATT
38916782 CTGTCATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (15 bp):
ATGATGTTCTAATTG
Found at i:38932695 original size:19 final size:19
Alignment explanation
Indices: 38932657--38932695 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38932647 CAACTCCTTC
*
38932657 CAAATTTTAGACGAACATT
1 CAAATTTTAGACGAAAATT
38932676 CAAA-TTTAGACGAATAATT
1 CAAATTTTAGACGAA-AATT
38932695 C
1 C
38932696 GACTCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (19 bp):
CAAATTTTAGACGAAAATT
Found at i:38932953 original size:14 final size:15
Alignment explanation
Indices: 38932927--38932955 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38932917 TTAAGGAACT
38932927 AATTTAGTTAAATTA
1 AATTTAGTTAAATTA
38932942 AATTTA-TTAAATTA
1 AATTTAGTTAAATTA
38932956 GATTGATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
AATTTAGTTAAATTA
Found at i:38951002 original size:27 final size:25
Alignment explanation
Indices: 38950971--38951021 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
38950961 ATAATTTAAT
38950971 AGTTTAGGTACTAATTCTGACAAAAAA
1 AGTTTAGGTACTAATT-TGA-AAAAAA
*
38950998 AGTTTAGGTATTAATTTGAAAAAA
1 AGTTTAGGTACTAATTTGAAAAAA
38951022 TTAGTATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 3 0.13
27 15 0.65
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (25 bp):
AGTTTAGGTACTAATTTGAAAAAAA
Found at i:38956765 original size:3 final size:3
Alignment explanation
Indices: 38956757--38956788 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
38956747 GGAAAGAGTA
38956757 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38956789 GGATGAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38957155 original size:9 final size:9
Alignment explanation
Indices: 38957141--38957184 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
38957131 TTTTGAACAA
38957141 TTTATTTTT
1 TTTATTTTT
*
38957150 TTTA-TTTC
1 TTTATTTTT
38957158 TTTATTTTT
1 TTTATTTTT
38957167 CTTTATTTTT
1 -TTTATTTTT
*
38957177 TTTCTTTT
1 TTTATTTT
38957185 CATATTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 14 0.47
10 9 0.30
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTATTTTT
Found at i:38957165 original size:14 final size:13
Alignment explanation
Indices: 38957140--38957179 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
38957130 TTTTTGAACA
38957140 ATTTATTTTTTTT
1 ATTTATTTTTTTT
*
38957153 ATTTCTTTATTTTT
1 ATTTATTT-TTTTT
*
38957167 CTTTATTTTTTTT
1 ATTTATTTTTTTT
38957180 CTTTTCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (13 bp):
ATTTATTTTTTTT
Found at i:38957169 original size:10 final size:10
Alignment explanation
Indices: 38957141--38957176 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
38957131 TTTTGAACAA
38957141 TTTATTTTT-
1 TTTATTTTTC
38957150 TTTA--TTTC
1 TTTATTTTTC
38957158 TTTATTTTTC
1 TTTATTTTTC
38957168 TTTATTTTT
1 TTTATTTTT
38957177 TTTCTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
7 3 0.12
8 4 0.17
9 4 0.17
10 13 0.54
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:38957185 original size:18 final size:18
Alignment explanation
Indices: 38957141--38957174 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
38957131 TTTTGAACAA
38957141 TTTATTTTT-TTTATTTC
1 TTTATTTTTCTTTATTTC
38957158 TTTATTTTTCTTTATTT
1 TTTATTTTTCTTTATTT
38957175 TTTTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTATTTTTCTTTATTTC
Found at i:38966892 original size:10 final size:10
Alignment explanation
Indices: 38966879--38966904 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38966869 AAAAAATCAT
38966879 AAATTTTTTA
1 AAATTTTTTA
38966889 AAATTTTTTA
1 AAATTTTTTA
38966899 AAATTT
1 AAATTT
38966905 CAATTATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
AAATTTTTTA
Found at i:38968923 original size:27 final size:30
Alignment explanation
Indices: 38968878--38968933 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 30
38968868 TTGGGTAAAT
38968878 TAAAGAAATATGTCGTTTTTATTAAATAAC
1 TAAAGAAATATGTCGTTTTTATTAAATAAC
*
38968908 TAAA-AAAT-TGTC-TTTTTTTTAAATAA
1 TAAAGAAATATGTCGTTTTTATTAAATAA
38968934 ATTAAGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 4 0.16
29 4 0.16
30 4 0.16
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (30 bp):
TAAAGAAATATGTCGTTTTTATTAAATAAC
Found at i:38968947 original size:22 final size:22
Alignment explanation
Indices: 38968909--38968958 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
38968899 TTAAATAACT
*
38968909 AAAAAATT--GTCTTTTTTTTA
1 AAAAAATTAAGTCTCTTTTTTA
*
38968929 AATAAATTAAGTCTCTTTTTTA
1 AAAAAATTAAGTCTCTTTTTTA
38968951 AAAAAATT
1 AAAAAATT
38968959 TTACCCGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
AAAAAATTAAGTCTCTTTTTTA
Found at i:38976397 original size:18 final size:18
Alignment explanation
Indices: 38976374--38976418 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
38976364 TTTTGGTTGC
* *
38976374 TGTTTTTTGTTATTTTTG
1 TGTTTTTTATTATTTTGG
*
38976392 TGTTTTTTATTGTTTTGG
1 TGTTTTTTATTATTTTGG
38976410 TGTTTTTTA
1 TGTTTTTTA
38976419 CGGTTTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.07, C:0.00, G:0.18, T:0.76
Consensus pattern (18 bp):
TGTTTTTTATTATTTTGG
Found at i:38976432 original size:19 final size:18
Alignment explanation
Indices: 38976386--38976428 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
38976376 TTTTTTGTTA
* **
38976386 TTTTTGTGTTTTTTATTG
1 TTTTGGTGTTTTTTACGG
38976404 TTTTGGTGTTTTTTACGG
1 TTTTGGTGTTTTTTACGG
38976422 TTTTGGT
1 TTTTGGT
38976429 TGTTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.05, C:0.02, G:0.23, T:0.70
Consensus pattern (18 bp):
TTTTGGTGTTTTTTACGG
Found at i:38976485 original size:12 final size:12
Alignment explanation
Indices: 38976422--38976541 Score: 57
Period size: 12 Copynumber: 9.9 Consensus size: 12
38976412 TTTTTTACGG
*
38976422 TTTTGGTTGTTA
1 TTTTTGTTGTTA
*
38976434 TTTTTG-TGTTG
1 TTTTTGTTGTTA
*
38976445 TTTTTGTTCTTA
1 TTTTTGTTGTTA
* *
38976457 TTTGCTGTTTTTA
1 TTT-TTGTTGTTA
* *
38976470 TTGTTATTTTTGTTG
1 -T-TT-TTGTTGTTA
**
38976485 TTTTTAATGTTA
1 TTTTTGTTGTTA
*
38976497 --TTTGCTGTTA
1 TTTTTGTTGTTA
* * *
38976507 TTTTTGCTATTG
1 TTTTTGTTGTTA
*
38976519 TTTTGGTTGTTA
1 TTTTTGTTGTTA
38976531 TTTTTGTTGTT
1 TTTTTGTTGTT
38976542 TGGATATTAT
Statistics
Matches: 79, Mismatches: 23, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
10 8 0.10
11 10 0.13
12 43 0.54
13 9 0.11
14 2 0.03
15 7 0.09
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:38976486 original size:21 final size:20
Alignment explanation
Indices: 38976428--38976499 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
38976418 ACGGTTTTGG
38976428 TTGTTATTTTTGTGTTGTTT-
1 TTGTTATTTTTGTGTT-TTTA
*
38976448 TTGTTCTTATTTGCTGTTTTTA
1 TTGTTATT-TTTG-TGTTTTTA
38976470 TTGTTATTTTTGTTGTTTTTA
1 TTGTTATTTTTG-TGTTTTTA
*
38976491 ATGTTATTT
1 TTGTTATTT
38976500 GCTGTTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
20 7 0.16
21 27 0.60
22 11 0.24
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTGTTATTTTTGTGTTTTTA
Found at i:38976498 original size:40 final size:42
Alignment explanation
Indices: 38976428--38976505 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 42
38976418 ACGGTTTTGG
**
38976428 TTGTTATTTTTGTGTTGTTTTTGTTCTTATTTGCTGTTTTTA
1 TTGTTATTTTTGTGTTGTTTTTAATCTTATTTGCTGTTTTTA
*
38976470 TTGTTA-TTTT-TGTTGTTTTTAATGTTATTTGCTGTT
1 TTGTTATTTTTGTGTTGTTTTTAATCTTATTTGCTGTT
38976506 ATTTTTGCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 23 0.70
41 4 0.12
42 6 0.18
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.71
Consensus pattern (42 bp):
TTGTTATTTTTGTGTTGTTTTTAATCTTATTTGCTGTTTTTA
Found at i:38976510 original size:21 final size:20
Alignment explanation
Indices: 38976454--38976510 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
38976444 GTTTTTGTTC
*
38976454 TTATTTGCTG-TTTTTATTG
1 TTATTTGCTGTTTTTTAATG
*
38976473 TTATTT-TTGTTGTTTTTAATG
1 TTATTTGCTG-T-TTTTTAATG
38976494 TTATTTGCTGTTATTTT
1 TTATTTGCTGTT-TTTT
38976511 TGCTATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.07
19 6 0.20
20 1 0.03
21 19 0.63
22 2 0.07
ACGTcount: A:0.12, C:0.04, G:0.14, T:0.70
Consensus pattern (20 bp):
TTATTTGCTGTTTTTTAATG
Found at i:38976753 original size:38 final size:39
Alignment explanation
Indices: 38976671--38976748 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
38976661 ATATAAAAAA
* * *
38976671 TTTTAATGTATTTTAAATTTATTTATTTTTTAATATTTG
1 TTTTAATGTATTTTAAATGTATTTATATATTAATATTTG
*
38976710 TTTTAATGT-TTTTAAGTGTATTTGATATATTATATATTT
1 TTTTAATGTATTTTAAATGTATTT-ATATATTA-ATATTT
38976749 TTTAAATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 12 0.36
39 15 0.45
40 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (39 bp):
TTTTAATGTATTTTAAATGTATTTATATATTAATATTTG
Found at i:38980784 original size:17 final size:17
Alignment explanation
Indices: 38980764--38980797 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38980754 TTTCAAATTT
*
38980764 TCAAATTTTAATTATTA
1 TCAAATTATAATTATTA
38980781 TCAAATTATAATTATTA
1 TCAAATTATAATTATTA
38980798 AATTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TCAAATTATAATTATTA
Found at i:38982549 original size:19 final size:19
Alignment explanation
Indices: 38982527--38982583 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
38982517 ATAAATTATA
38982527 AATTTTTATAAAA-ATTTTG
1 AATTTTTA-AAAATATTTTG
38982546 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAA-TATTTTG
*
38982565 AATTTTTGAAAATTATTTT
1 AATTTTT-AAAAATATTTT
38982584 TTATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 10 0.30
20 10 0.30
21 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
AATTTTTAAAAATATTTTG
Done.