Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 3 of 230
Found at i:771613 original size:125 final size:124
Alignment explanation
Indices: 771204--771640 Score: 596
Period size: 124 Copynumber: 3.5 Consensus size: 124
771194 ATAAAATCAA
* * * * * * * * *
771204 AGCAGGATG-ATTATCAGAAGGATTTTTGCAGTCGCGCCCGCATGTACGCGCTTTTGCTACAGTA
1 AGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
* *
771268 GGTCCTG-GAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCT
66 GGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCT
* * *
771326 ACCAGGATGTTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTA
1 AGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
* * *
771391 GGTCCTGAAAAAATTA-TT-GAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTCA
66 GGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAATCGCTTCT
* *
771450 AGCAGGATGCTATT-TGAGAAGAATTTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
771514 TGGTCCTGAAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAATCACTTCT
65 AGGTCCTGAAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCT
*
771575 AGCAGGATGCTTTATGAGAAGAATTTGTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACAGTA
1 AGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
771640 G
66 G
771641 CATGTTTGGG
Statistics
Matches: 275, Mismatches: 31, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
122 34 0.12
123 54 0.20
124 84 0.31
125 75 0.27
126 2 0.01
127 26 0.09
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (124 bp):
AGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
GGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCT
Found at i:771858 original size:51 final size:51
Alignment explanation
Indices: 771811--771943 Score: 223
Period size: 51 Copynumber: 2.6 Consensus size: 51
771801 AAAAATAGGG
*
771811 ATTTAAGAGAAATTTAAAAGGAAATTGAGAGCTAATTGAGATTAAATATAA
1 ATTTGAGAGAAATTTAAAAGGAAATTGAGAGCTAATTGAGATTAAATATAA
* *
771862 ATTTGAGAGAAATTTAGAAGAAAATTGAGAGCTAATTGAGATTAAATATAA
1 ATTTGAGAGAAATTTAAAAGGAAATTGAGAGCTAATTGAGATTAAATATAA
771913 ATTTGAGAGAAATTTAGAAA-GAAATTGAGAG
1 ATTTGAGAGAAATTTA-AAAGGAAATTGAGAG
771944 GAAATTTGAG
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 74 0.97
52 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.29
Consensus pattern (51 bp):
ATTTGAGAGAAATTTAAAAGGAAATTGAGAGCTAATTGAGATTAAATATAA
Found at i:771953 original size:12 final size:12
Alignment explanation
Indices: 771911--771955 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
771901 GATTAAATAT
771911 AAATTTGAGA-G
1 AAATTTGAGAGG
*
771922 AAATTT-AGAAAG
1 AAATTTGAG-AGG
771934 AAA-TTGAGAGG
1 AAATTTGAGAGG
771945 AAATTTGAGAG
1 AAATTTGAGAG
771956 AGGATTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 2 0.07
11 14 0.48
12 13 0.45
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (12 bp):
AAATTTGAGAGG
Found at i:780185 original size:31 final size:31
Alignment explanation
Indices: 780137--780222 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
780127 GGGGCCTTGG
* * *
780137 TCCCCAAAGTTTTTGAAAATTTTAGTTA-TA
1 TCCCTAAAATTTTTGAAAATTTTAATTAGTA
* * * *
780167 TCCTTAAATTTTTCTGAAATTTTTAATTAGGTC
1 TCCCTAAAATTTT-TGAAAATTTTAATTA-GTA
780200 TCCCTAAAATTTTTGAAAATTTT
1 TCCCTAAAATTTTTGAAAATTTT
780223 TAAATATTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
30 10 0.23
31 13 0.30
32 9 0.20
33 12 0.27
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (31 bp):
TCCCTAAAATTTTTGAAAATTTTAATTAGTA
Found at i:780223 original size:33 final size:31
Alignment explanation
Indices: 780137--780225 Score: 83
Period size: 33 Copynumber: 2.8 Consensus size: 31
780127 GGGGCCTTGG
* * *
780137 TCCCCAAAGTTTTTGAAAA-TTTTAGTTATA
1 TCCCTAAAATTTTTGAAAATTTTTAATTATA
* * *
780167 TCCTTAAATTTTTCTG-AAATTTTTAATTAGGTC
1 TCCCTAAAATTTT-TGAAAATTTTTAATTA--TA
780200 TCCCTAAAATTTTTGAAAATTTTTAA
1 TCCCTAAAATTTTTGAAAATTTTTAA
780226 ATATTTCAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 13 0.28
31 10 0.21
32 2 0.04
33 22 0.47
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (31 bp):
TCCCTAAAATTTTTGAAAATTTTTAATTATA
Found at i:781665 original size:18 final size:20
Alignment explanation
Indices: 781630--781666 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
781620 TTTTACTATC
*
781630 TTTTCTATTTTAATAAATAT
1 TTTTCTATTTGAATAAATAT
781650 TTTTCT-TTTGAA-AAATA
1 TTTTCTATTTGAATAAATA
781667 ACTTGATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 5 0.31
20 6 0.38
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTCTATTTGAATAAATAT
Found at i:781804 original size:3 final size:3
Alignment explanation
Indices: 781796--781826 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
781786 AATTAATTAC
781796 ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
781827 TTACATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:783488 original size:30 final size:28
Alignment explanation
Indices: 783454--783524 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
783444 ACGATTGAAC
*
783454 TTAAATTTTAAAATATTAAAAATA-AAGAGA
1 TTAAATTCTAAAA-A-TAAAAATATAAGA-A
*
783484 TTAAATTCTAAGAAATAAAAGTATAAGAA
1 TTAAATTCTAA-AAATAAAAATATAAGAA
783513 TTAAATTCTAAA
1 TTAAATTCTAAA
783525 TTTGTGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 1 0.03
29 19 0.51
30 15 0.41
31 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (28 bp):
TTAAATTCTAAAAATAAAAATATAAGAA
Found at i:784546 original size:17 final size:17
Alignment explanation
Indices: 784526--784583 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
784516 TTATATTAGT
784526 AATAAAATTAATAATAA
1 AATAAAATTAATAATAA
*
784543 AATAAAAATTATATAATATTC
1 AAT-AAAATTA-ATAATA--A
784564 AA-AAAA-TAATAATAA
1 AATAAAATTAATAATAA
784579 AATAA
1 AATAA
784584 TAACAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 9 0.26
18 9 0.26
19 10 0.29
21 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAAATTAATAATAA
Found at i:784580 original size:11 final size:11
Alignment explanation
Indices: 784525--784586 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
784515 TTTATATTAG
784525 TAATAAAATTAA
1 TAATAAAA-TAA
784537 TAATAAAATAA
1 TAATAAAATAA
* *
784548 AAATTATATAATAT
1 TAA-TA-A-AATAA
784562 TCAA-AAAATAA
1 T-AATAAAATAA
784573 TAATAAAATAA
1 TAATAAAATAA
784584 TAA
1 TAA
784587 CAAATCAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
10 2 0.05
11 20 0.49
12 11 0.27
13 2 0.05
14 4 0.10
15 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:789259 original size:23 final size:24
Alignment explanation
Indices: 789227--789273 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
789217 CAAATATAAT
*
789227 AAATATTTTTATT-TTTTATTTTA
1 AAATACTTTTATTATTTTATTTTA
* *
789250 AAATACTTTTTTTATTTTTTTTTA
1 AAATACTTTTATTATTTTATTTTA
789274 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
AAATACTTTTATTATTTTATTTTA
Found at i:789278 original size:19 final size:19
Alignment explanation
Indices: 789256--789309 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
789246 TTTAAAATAC
789256 TTTTTTT-ATTTTTTTTTA
1 TTTTTTTAATTTTTTTTTA
** *
789274 TTTTTAAAATATTTTTTTA
1 TTTTTTTAATTTTTTTTTA
789293 TTTTTTTAATTTTTTTT
1 TTTTTTTAATTTTTTTT
789310 GGTGTTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTAATTTTTTTTTA
Found at i:789286 original size:21 final size:21
Alignment explanation
Indices: 789262--789301 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
789252 ATACTTTTTT
789262 TATTTTTTT-TTATTTTTAAAA
1 TATTTTTTTATT-TTTTTAAAA
789283 TATTTTTTTATTTTTTTAA
1 TATTTTTTTATTTTTTTAA
789302 TTTTTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTTTTTTATTTTTTTAAAA
Found at i:789308 original size:30 final size:30
Alignment explanation
Indices: 789238--789299 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
789228 AATATTTTTA
789238 TTTTTTA-TTTTAAAATACTTTTTTTATTT
1 TTTTTTATTTTTAAAATACTTTTTTTATTT
789267 TTTTTTATTTTTAAAATA-TTTTTTTATTT
1 TTTTTTATTTTTAAAATACTTTTTTTATTT
789296 TTTT
1 TTTT
789300 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTTATTTTTAAAATACTTTTTTTATTT
Found at i:790292 original size:28 final size:29
Alignment explanation
Indices: 790261--790315 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
790251 TTGAAAGAAA
*
790261 ATTTAACT-TTTAAGAT-ATAAAAATAAAT
1 ATTTAA-TATTTAAAATAATAAAAATAAAT
*
790289 ATTTTATATTTAAAATAATAAAAATAA
1 ATTTAATATTTAAAATAATAAAAATAA
790316 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.04
28 12 0.52
29 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
ATTTAATATTTAAAATAATAAAAATAAAT
Found at i:794183 original size:15 final size:15
Alignment explanation
Indices: 794163--794195 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
794153 CTACCTTTAC
794163 AATATCCCAATTAGA
1 AATATCCCAATTAGA
794178 AATATCCCAATTAGA
1 AATATCCCAATTAGA
794193 AAT
1 AAT
794196 CCCCACATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (15 bp):
AATATCCCAATTAGA
Found at i:796801 original size:17 final size:17
Alignment explanation
Indices: 796779--796819 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
796769 CCGGTTCTCG
796779 ATTCGACTAGTTTAACT
1 ATTCGACTAGTTTAACT
796796 ATTCGACTAGTTTAACT
1 ATTCGACTAGTTTAACT
796813 AGTTCGA
1 A-TTCGA
796820 TAGCCAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (17 bp):
ATTCGACTAGTTTAACT
Found at i:800030 original size:19 final size:20
Alignment explanation
Indices: 800003--800044 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
799993 TTGCTATTTG
* *
800003 AAAATTTTTATTAAGCTCCA
1 AAAATTTTAATTAAGCCCCA
800023 AAAATTTTAATTAAGCCCCA
1 AAAATTTTAATTAAGCCCCA
800043 AA
1 AA
800045 TGTTTTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATTTTAATTAAGCCCCA
Found at i:800060 original size:30 final size:30
Alignment explanation
Indices: 800023--800095 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
800013 TTAAGCTCCA
800023 AAAATTTTAATTAAGCC-CCA-AATGTTTTTG
1 AAAATTTTAATTAAGCCTCCAGAA--TTTTTG
* * *
800053 GAAATTTTCATTAAGCCTCTAGAATTTTTG
1 AAAATTTTAATTAAGCCTCCAGAATTTTTG
800083 AAAATTTTAATTA
1 AAAATTTTAATTA
800096 CCCCCTCCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 32 0.89
31 2 0.06
32 2 0.06
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (30 bp):
AAAATTTTAATTAAGCCTCCAGAATTTTTG
Found at i:801388 original size:13 final size:14
Alignment explanation
Indices: 801360--801394 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
801350 TAATATAAAC
801360 ATAAATATTCATTTT
1 ATAAAT-TTCATTTT
801375 ATAAATTT-ATTTT
1 ATAAATTTCATTTT
801388 ATAAATT
1 ATAAATT
801395 ATAATAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
14 2 0.10
15 6 0.30
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAAATTTCATTTT
Found at i:802037 original size:20 final size:19
Alignment explanation
Indices: 801953--802037 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 19
801943 TAAGTCTTTG
801953 AATTTTATTTTTATTTATTA
1 AATTTTATTTTTATTT-TTA
* *
801973 AATTATT-TGTTTAGACTTTTA
1 AATT-TTAT-TTT-TATTTTTA
* * * *
801994 GACTTTAGTTTTAGTTTTA
1 AATTTTATTTTTATTTTTA
802013 GAATTTTATTTTTATTTATTA
1 -AATTTTATTTTTATTT-TTA
802034 AATT
1 AATT
802038 ATTTATGATT
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
19 6 0.12
20 26 0.54
21 13 0.27
22 3 0.06
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.62
Consensus pattern (19 bp):
AATTTTATTTTTATTTTTA
Found at i:805821 original size:22 final size:22
Alignment explanation
Indices: 805793--805837 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
805783 TGGGAATATA
*
805793 CAATTAGTCACTCAATTATTAG
1 CAATTAGCCACTCAATTATTAG
805815 CAATTAGCCACTCAATTATTAG
1 CAATTAGCCACTCAATTATTAG
805837 C
1 C
805838 GTGCTCATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (22 bp):
CAATTAGCCACTCAATTATTAG
Found at i:807240 original size:15 final size:14
Alignment explanation
Indices: 807215--807245 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
807205 ATTAAAACTA
807215 TAAAAATAATTAAT
1 TAAAAATAATTAAT
807229 TAAAAATAAATTAAT
1 TAAAAAT-AATTAAT
807244 TA
1 TA
807246 GTAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAAATAATTAAT
Found at i:807364 original size:14 final size:14
Alignment explanation
Indices: 807345--807371 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
807335 TAATTCAAAA
807345 ATAAAAATATTAAT
1 ATAAAAATATTAAT
807359 ATAAAAATATTAA
1 ATAAAAATATTAA
807372 AATTTTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAATATTAAT
Found at i:807435 original size:16 final size:17
Alignment explanation
Indices: 807414--807451 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
807404 CGTATAATTC
*
807414 AAAAATAAAAATA-TTT
1 AAAAATAAAAAAATTTT
807430 AAAAATAAAAAAATTTT
1 AAAAATAAAAAAATTTT
807447 AAAAA
1 AAAAA
807452 AAGTTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATAAAAAAATTTT
Found at i:807440 original size:17 final size:16
Alignment explanation
Indices: 807414--807451 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
807404 CGTATAATTC
807414 AAAAAT-AAAAATATTT
1 AAAAATAAAAAAT-TTT
807430 AAAAATAAAAAAATTTT
1 AAAAAT-AAAAAATTTT
807447 AAAAA
1 AAAAA
807452 AAGTTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAAAATTTT
Found at i:811157 original size:3 final size:3
Alignment explanation
Indices: 811151--811179 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
811141 ATGATGATGA
811151 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
811180 TTTGTTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:816396 original size:24 final size:24
Alignment explanation
Indices: 816364--816410 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
816354 TTTGAGTACT
*
816364 TCTGATCAGTAACCAGTGACAAGA
1 TCTGATCAGTAACAAGTGACAAGA
*
816388 TCTGATCAGTGACAAGTGACAAG
1 TCTGATCAGTAACAAGTGACAAG
816411 TGATAAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (24 bp):
TCTGATCAGTAACAAGTGACAAGA
Found at i:818829 original size:24 final size:24
Alignment explanation
Indices: 818794--818842 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
818784 TATATATATG
818794 AAACTTTAATTTTGATTCAATTGT
1 AAACTTTAATTTTGATTCAATTGT
* *
818818 AAACTTTGATTTTGATTTAATTGT
1 AAACTTTAATTTTGATTCAATTGT
818842 A
1 A
818843 TACATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (24 bp):
AAACTTTAATTTTGATTCAATTGT
Found at i:851933 original size:23 final size:24
Alignment explanation
Indices: 851889--851933 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
851879 ATTAAAATGG
*
851889 AAAAAAATACATTTTAACTTTCAT
1 AAAAAAATACAATTTAACTTTCAT
*
851913 AAAAATATACAATTTAA-TTTC
1 AAAAAAATACAATTTAACTTTC
851934 GACTCTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAAAAATACAATTTAACTTTCAT
Found at i:852294 original size:13 final size:13
Alignment explanation
Indices: 852270--852304 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
852260 TATTATTTTT
852270 AAAATT-TTTAAA
1 AAAATTATTTAAA
852282 AAAATTATTTAAA
1 AAAATTATTTAAA
*
852295 AAAATGATTT
1 AAAATTATTT
852305 TTATAGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
AAAATTATTTAAA
Found at i:870608 original size:30 final size:30
Alignment explanation
Indices: 870573--870636 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
870563 ATATACCCGA
* *
870573 TCCTCCACTCCTTAGCTCCTTTGTTAGTTC
1 TCCTCCACGCCTTAGCTCCTTTGTTACTTC
870603 TCCTCCACGCCTTAGCTCCTTTGTTACTTC
1 TCCTCCACGCCTTAGCTCCTTTGTTACTTC
870633 TCCT
1 TCCT
870637 TAGATCATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.09, C:0.39, G:0.09, T:0.42
Consensus pattern (30 bp):
TCCTCCACGCCTTAGCTCCTTTGTTACTTC
Found at i:871036 original size:5 final size:5
Alignment explanation
Indices: 871026--871061 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
871016 TTAACTAAGA
871026 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT T
1 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT T
871062 CTATTGGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (5 bp):
TGGGT
Found at i:871579 original size:5 final size:5
Alignment explanation
Indices: 871569--871600 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
871559 TAAGTATAAC
871569 TAATT TAATT TAATT TAATT TAATT TCAATT T
1 TAATT TAATT TAATT TAATT TAATT T-AATT T
871601 GTTGGGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:873084 original size:14 final size:14
Alignment explanation
Indices: 873042--873084 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
873032 AAAATAGAGT
873042 AATTAAATTACTAAA
1 AATTAAATT-CTAAA
* * *
873057 AATAAAAATATAAA
1 AATTAAATTCTAAA
873071 AATTAAATTCTAAA
1 AATTAAATTCTAAA
873085 TTTAAAAAGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTAAATTCTAAA
Found at i:873092 original size:29 final size:30
Alignment explanation
Indices: 873027--873092 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
873017 TTTTAAAAAT
**
873027 TTTAAAAAATAGAGTAATTAAATTACTAAA
1 TTTAAAAAATAGAAAAATTAAATTACTAAA
** *
873057 AAT-AAAAATATAAAAATTAAATT-CTAAA
1 TTTAAAAAATAGAAAAATTAAATTACTAAA
873085 TTTAAAAA
1 TTTAAAAA
873093 GGTACAGGAC
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
28 6 0.21
29 21 0.75
30 1 0.04
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (30 bp):
TTTAAAAAATAGAAAAATTAAATTACTAAA
Found at i:873334 original size:11 final size:11
Alignment explanation
Indices: 873318--873343 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
873308 AATTTTTAAA
873318 TTTTAAAATAC
1 TTTTAAAATAC
873329 TTTTAAAATAC
1 TTTTAAAATAC
873340 TTTT
1 TTTT
873344 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:873375 original size:20 final size:22
Alignment explanation
Indices: 873350--873396 Score: 80
Period size: 20 Copynumber: 2.2 Consensus size: 22
873340 TTTTTTTAAA
873350 TTTTTTTAA-TTTTAAAAT-AT
1 TTTTTTTAATTTTTAAAATAAT
873370 TTTTTTTAATTTTTAAAATAAT
1 TTTTTTTAATTTTTAAAATAAT
873392 TTTTT
1 TTTTT
873397 GTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTTTAATTTTTAAAATAAT
Found at i:873402 original size:21 final size:20
Alignment explanation
Indices: 873348--873402 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
873338 ACTTTTTTTA
*
873348 AATTTTTTTAATTTTAAAAT
1 AATTTTTTTATTTTTAAAAT
*
873368 ATTTTTTTTAATTTTTAAAAT
1 AATTTTTTT-ATTTTTAAAAT
873389 AATTTTTTGTATTT
1 AATTTTTT-TATTT
873403 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.27
21 21 0.70
22 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTTTTTTATTTTTAAAAT
Found at i:874337 original size:23 final size:21
Alignment explanation
Indices: 874291--874339 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
874281 CTCTCTGAAT
*
874291 AAAAATTAAATAAATCCCCAA
1 AAAAATTAAATAAATACCCAA
*
874312 AAAAATTAAAAATAAA-ACCCAG
1 AAAAATT--AAATAAATACCCAA
874334 AAAAAT
1 AAAAAT
874340 AGTAGCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAAATTAAATAAATACCCAA
Found at i:875347 original size:215 final size:215
Alignment explanation
Indices: 874967--875469 Score: 718
Period size: 215 Copynumber: 2.3 Consensus size: 215
874957 CGAACATAGG
* * * *
874967 TACTACAAGAAAAATGAAGAGTCTGAGCATCATAGCTTAGCATGAACTAAAACTAGGTAATGGCA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
* * *
875032 GTGATAAAATCTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCCGATTTGGGTGT
66 GTGATAAAATCGTGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCCGATTTGGGTGT
** * * * ***
875097 AGTTGTCCAATACTGGTAGTGTCTGATATGAGTTTAGAGGTTGTATCTCTGTATTTGTGTGTCGG
131 AGTTGTCCAATACTAATAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTATTACAGTGTCGG
875162 ACATGAGGGTCAGACACAGA
196 ACATGAGGGTCAGACACAGA
* *
875182 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGTTTAGCACGAACCAAAACTAGGTAATGGTA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
* * * * *
875247 GTGATAAAATCGTGTTTTCTTATTTGGAAATTTACTTAGCACCTGTATTACTCGGATTTGGGTGT
66 GTGATAAAATCGTGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCCGATTTGGGTGT
** *
875312 AGTTGTCTGATACTAATAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTATTACAGTGTTGG
131 AGTTGTCCAATACTAATAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTATTACAGTGTCGG
* *
875377 ACATGAGTGTCAGGCACAGA
196 ACATGAGGGTCAGACACAGA
* * * * *
875397 TACTTAAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGGACAAACTAAAACTATGTAATGGTA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
875462 GTGATAAA
66 GTGATAAA
875470 GTCTTGGAAC
Statistics
Matches: 254, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
215 254 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (215 bp):
TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
GTGATAAAATCGTGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCCGATTTGGGTGT
AGTTGTCCAATACTAATAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTATTACAGTGTCGG
ACATGAGGGTCAGACACAGA
Found at i:878982 original size:1 final size:1
Alignment explanation
Indices: 878976--879023 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
878966 CCCCAAATTA
* * * * *
878976 TTTTTTTCTTTCTTTTTTTTTTGTTTTTTTGTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
879024 ATGCTTTAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:878996 original size:15 final size:14
Alignment explanation
Indices: 878976--879023 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
878966 CCCCAAATTA
*
878976 TTTTTTTCTTTCTTT
1 TTTTTTTGTTT-TTT
878991 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
*
879005 TGTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
879019 TTTTT
1 TTTTT
879024 ATGCTTTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (14 bp):
TTTTTTTGTTTTTT
Found at i:880046 original size:12 final size:12
Alignment explanation
Indices: 880029--880089 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
880019 CCAAATAAGT
880029 AATAAATAATAA
1 AATAAATAATAA
880041 AATAAAGTAAT-A
1 AATAAA-TAATAA
*
880053 AATAAAGTAA-AG
1 AATAAA-TAATAA
880065 AA-AAATAATAA
1 AATAAATAATAA
880076 TAATAAAATAATAA
1 -AAT-AAATAATAA
880090 TAAAAATTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.07
11 4 0.10
12 21 0.51
13 4 0.10
14 9 0.22
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:880050 original size:20 final size:20
Alignment explanation
Indices: 880021--880086 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
880011 ATTAATATCC
880021 AAAT-AAGTAATAAATAATA
1 AAATAAAGTAATAAATAATA
880040 AAATAAAGTAATAAATAAAGTA
1 AAATAAAGTAATAAAT-AA-TA
*
880062 AAGA-AAAATAAT-AATAATA
1 AA-ATAAAGTAATAAATAATA
880081 AAATAA
1 AAATAA
880087 TAATAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
18 1 0.02
19 10 0.24
20 13 0.32
21 5 0.12
22 11 0.27
23 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (20 bp):
AAATAAAGTAATAAATAATA
Found at i:880058 original size:17 final size:17
Alignment explanation
Indices: 880036--880094 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
880026 AGTAATAAAT
880036 AATAAAATAAAGTAATA
1 AATAAAATAAAGTAATA
* * *
880053 AATAAAGTAAAGAAAAA
1 AATAAAATAAAGTAATA
*
880070 TAATAATAATAAAATAAT-
1 -AATAA-AATAAAGTAATA
880088 AATAAAA
1 AATAAAA
880095 ATTGGGTTGC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 2 0.06
17 19 0.58
18 5 0.15
19 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (17 bp):
AATAAAATAAAGTAATA
Found at i:881066 original size:16 final size:16
Alignment explanation
Indices: 881047--881116 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
881037 TTTGGTTCGC
* *
881047 TGTATTGGATTAGAGC
1 TGTAATGGATTAGAGG
*
881063 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
881079 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
*
881095 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
881111 TGTAAT
1 TGTAAT
881117 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.30, C:0.01, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:881200 original size:39 final size:43
Alignment explanation
Indices: 881095--881204 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
881085 GGATTAGAGG
881095 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
881140 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
881180 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
881205 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:881367 original size:16 final size:16
Alignment explanation
Indices: 881330--881371 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
881320 TTAATCATAT
*
881330 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
881346 TT-AAATATATTATAA
1 TTAAAATATATTATAA
881361 TTAAAATATAT
1 TTAAAATATAT
881372 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:881378 original size:14 final size:15
Alignment explanation
Indices: 881339--881380 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
881329 TTTAAACATA
*
881339 ATTATTATTAAATAT
1 ATTATAATTAAATAT
881354 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
881368 A-TATAATTTAATA
1 ATTATAATTAAATA
881381 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:881430 original size:61 final size:61
Alignment explanation
Indices: 881365--881552 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
881355 TTATAATTAA
*
881365 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
881426 AATATATGATACT-ATAAAA-TATAAATTAAT--ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTATTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
881485 AATATATAATTTAATAATATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
881546 AATATAT
1 AATATAT
881553 GACTGTTATT
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 23 0.24
61 38 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:881474 original size:16 final size:17
Alignment explanation
Indices: 881453--881490 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
881443 AATATAAATT
*
881453 AATATAATTATTATT-A
1 AATATAATTATAATTAA
881469 AATAT-ATTATAATTAA
1 AATATAATTATAATTAA
881485 AATATA
1 AATATA
881491 TAATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAATTATAATTAA
Found at i:881481 original size:120 final size:120
Alignment explanation
Indices: 881336--881554 Score: 420
Period size: 120 Copynumber: 1.8 Consensus size: 120
881326 ATATTTAAAC
*
881336 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAATAT
881401 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAAT
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAAT
*
881456 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAATATTATTAATAATCAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAATAT
881521 TCTTATATGAATTTACTCAAATCATAATATATGA
66 TCTTATATGAATTTACTCAAATCATAATATATGA
881555 CTGTTATTGC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAATAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAAT
Found at i:881491 original size:16 final size:16
Alignment explanation
Indices: 881449--881491 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
881439 ATAAAATATA
*
881449 AATTAATATA-ATTAT
1 AATTAAAATATATTAT
*
881464 TATT-AAATATATTAT
1 AATTAAAATATATTAT
881479 AATTAAAATATAT
1 AATTAAAATATAT
881492 AATTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:881499 original size:44 final size:43
Alignment explanation
Indices: 881426--881509 Score: 109
Period size: 43 Copynumber: 1.9 Consensus size: 43
881416 CTCAAATCAT
*
881426 AATATATGATACTATAAAATATAAATTAAT-ATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAATAAT-ATTATTATTA
*
881469 AATATATTATAAT-TAAAATATATAATTTAATAATATTATTA
1 AATATATGATAATATAAAATATA-AA-TTAATAATATTATTA
881510 ATAATCAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
42 9 0.25
43 13 0.36
44 12 0.33
45 2 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAATAATATTATTATTA
Found at i:892121 original size:12 final size:12
Alignment explanation
Indices: 892104--892128 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
892094 AAACAGGGAT
892104 TCATCATCTTCA
1 TCATCATCTTCA
892116 TCATCATCTTCA
1 TCATCATCTTCA
892128 T
1 T
892129 TCGGTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCATCATCTTCA
Found at i:894421 original size:31 final size:31
Alignment explanation
Indices: 894352--894421 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
894342 ATTAACAGTC
* *
894352 CAGTGGCTTAAATAAAAATTTTCAAATAGTT
1 CAGTGACTTAAATAAAAATTTTCAAATAATT
* *
894383 CAATGACTTAAATGAAAATTTTCAAATAATT
1 CAGTGACTTAAATAAAAATTTTCAAATAATT
*
894414 TAGTGACT
1 CAGTGACT
894422 ATTTTGTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAATTTTCAAATAATT
Found at i:896470 original size:57 final size:57
Alignment explanation
Indices: 896409--896523 Score: 126
Period size: 58 Copynumber: 2.0 Consensus size: 57
896399 AAAAAAATAC
* *
896409 AAATTT-GAACAGTTG-GCTGACCATTTTATAACCTTTCATAGTTAGGTAACCAAAAAA
1 AAATTTAGAACAATTGTG-TGACCATTTTA-AACCTTTCATAGTTAGATAACCAAAAAA
* * * * *
896466 AAATTTACTAATAATTGTGTGACTATTTTAAACTTTTCATAGTTAGATGACCAAAAAA
1 AAATTTA-GAACAATTGTGTGACCATTTTAAACCTTTCATAGTTAGATAACCAAAAAA
896524 TAAAAATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
57 6 0.12
58 25 0.52
59 16 0.33
60 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (57 bp):
AAATTTAGAACAATTGTGTGACCATTTTAAACCTTTCATAGTTAGATAACCAAAAAA
Found at i:897415 original size:17 final size:18
Alignment explanation
Indices: 897388--897421 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
897378 TTTATATATT
*
897388 AAATTGCATATTAAAATA
1 AAATTGCATATAAAAATA
897406 AAATTG-ATATAAAAAT
1 AAATTGCATATAAAAAT
897422 TTGTTATTTA
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:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (18 bp):
AAATTGCATATAAAAATA
Found at i:903145 original size:31 final size:31
Alignment explanation
Indices: 903083--903146 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
903073 AAAATAGCAG
* * * *
903083 TTCGACTTTTTTTGAAAGGTTGATGATCAAA
1 TTCGACTCTTTTTAAAAGATTGATGACCAAA
903114 TTCGACTCTTTTTAAAAGATTGA-GAGCCAAA
1 TTCGACTCTTTTTAAAAGATTGATGA-CCAAA
903145 TT
1 TT
903147 TAGCTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (31 bp):
TTCGACTCTTTTTAAAAGATTGATGACCAAA
Found at i:904437 original size:17 final size:17
Alignment explanation
Indices: 904415--904447 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
904405 AAGAAAATAA
904415 TAATAAA-AGAAGTAAAC
1 TAATAAATAGAA-TAAAC
904432 TAATAAATAGAATAAA
1 TAATAAATAGAATAAA
904448 GGGTAAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (17 bp):
TAATAAATAGAATAAAC
Found at i:908522 original size:40 final size:40
Alignment explanation
Indices: 908467--908563 Score: 160
Period size: 40 Copynumber: 2.4 Consensus size: 40
908457 ATGCATGCAT
* *
908467 GCATACATGCATACATATTAAG-ACAAATGTAAAAAGAGTG
1 GCATGCATGCATACATATTAAGAAAAAATGTAAAAA-AGTG
908507 GCATGCATGCATACATATTAAGAAAAAATGTAAAAAAGTG
1 GCATGCATGCATACATATTAAGAAAAAATGTAAAAAAGTG
908547 GCATGCATGCATACATA
1 GCATGCATGCATACATA
908564 CATATATACA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 42 0.78
41 12 0.22
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (40 bp):
GCATGCATGCATACATATTAAGAAAAAATGTAAAAAAGTG
Found at i:912641 original size:31 final size:31
Alignment explanation
Indices: 912606--912666 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
912596 ACAACCCAAT
912606 GATTTAAAT-AAAA-ATTTACGAATAGTTCAAC
1 GATTTAAATCAAAACATTTA--AATAGTTCAAC
*
912637 GATTTAAATCAAAACTTTTAAATAGTTCAA
1 GATTTAAATCAAAACATTTAAATAGTTCAA
912667 TAATCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 19 0.70
32 4 0.15
33 4 0.15
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (31 bp):
GATTTAAATCAAAACATTTAAATAGTTCAAC
Found at i:921864 original size:38 final size:39
Alignment explanation
Indices: 921788--921870 Score: 123
Period size: 38 Copynumber: 2.1 Consensus size: 39
921778 TATGAATCAG
*
921788 ATTGCATTTTACCTTCTATACTAAAAAAAAAAAAGAAATAA
1 ATTGCATTTTACCTTATATACT--AAAAAAAAAAGAAATAA
*
921829 ATTGTATTTTACCTTATATACT-AAAAAAAAAGAAATAA
1 ATTGCATTTTACCTTATATACTAAAAAAAAAAGAAATAA
921867 ATTG
1 ATTG
921871 GTTATTCCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 20 0.50
41 20 0.50
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (39 bp):
ATTGCATTTTACCTTATATACTAAAAAAAAAAGAAATAA
Found at i:922380 original size:31 final size:30
Alignment explanation
Indices: 922340--922399 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
922330 GTAAAAATTA
* *
922340 AAATTATACATAAATTTTGATTCAATATAT
1 AAATTATACATAAACTTTCATTCAATATAT
* *
922370 AAATTGATACATGAACTTTCATTTAATATA
1 AAATT-ATACATAAACTTTCATTCAATATA
922400 ATTATACATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (30 bp):
AAATTATACATAAACTTTCATTCAATATAT
Found at i:922897 original size:33 final size:30
Alignment explanation
Indices: 922860--922931 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 30
922850 TATATTGTGA
*
922860 TCACTGAACCATTTGAAAGTTTTCAGTTATAAC
1 TCACTGAACCATTT-AAAATTTTCA-TT-TAAC
* * *
922893 TCACTGAACTATTTAAAATTTTTATTTAAG
1 TCACTGAACCATTTAAAATTTTCATTTAAC
922923 TCACTGAAC
1 TCACTGAAC
922932 TATTAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.34
31 2 0.06
32 8 0.23
33 13 0.37
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (30 bp):
TCACTGAACCATTTAAAATTTTCATTTAAC
Found at i:922929 original size:30 final size:33
Alignment explanation
Indices: 922860--922935 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 33
922850 TATATTGTGA
* *
922860 TCACTGAACCATTTGAAAGTTTTCAGTTATAAC
1 TCACTGAACTATTTGAAAATTTTCAGTTATAAC
* *
922893 TCACTGAACTATTT-AAAATTTTTA-TT-TAAG
1 TCACTGAACTATTTGAAAATTTTCAGTTATAAC
922923 TCACTGAACTATT
1 TCACTGAACTATT
922936 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 16 0.41
31 2 0.05
32 8 0.21
33 13 0.33
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (33 bp):
TCACTGAACTATTTGAAAATTTTCAGTTATAAC
Found at i:926482 original size:24 final size:24
Alignment explanation
Indices: 926450--926499 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
926440 ATACAATTAC
*
926450 ATATTAGACTAAAATTAATGTATA
1 ATATTAGACCAAAATTAATGTATA
*
926474 ATATTAGACCAGAATTAATGTATA
1 ATATTAGACCAAAATTAATGTATA
926498 AT
1 AT
926500 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (24 bp):
ATATTAGACCAAAATTAATGTATA
Found at i:927328 original size:21 final size:21
Alignment explanation
Indices: 927295--927335 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
927285 CTTGATGTGA
927295 ATTAAAAATAATTATTTATTC
1 ATTAAAAATAATTATTTATTC
927316 ATTATAAAA-AATTATTTATT
1 ATTA-AAAATAATTATTTATT
927336 TAGATGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAAAAATAATTATTTATTC
Found at i:950409 original size:34 final size:31
Alignment explanation
Indices: 950371--950442 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 31
950361 CTTAACAACC
*
950371 CAATGACTTAAATAAAAAAAACTTTTAAATAATT
1 CAATGACTTAAAT---AAAAACTTTCAAATAATT
*
950405 CAATGATTTAAATAAAAACTTTCAAATAATT
1 CAATGACTTAAATAAAAACTTTCAAATAATT
950436 CAATGAC
1 CAATGAC
950443 CATTTTGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 23 0.66
34 12 0.34
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTTTCAAATAATT
Found at i:950422 original size:31 final size:30
Alignment explanation
Indices: 950383--950441 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
950373 ATGACTTAAA
*
950383 TAAAAAAAACTTTTAAATAATTCAATGATT
1 TAAAAAAAACTTTCAAATAATTCAATGATT
950413 TAAATAAAAACTTTCAAATAATTCAATGA
1 TAAA-AAAAACTTTCAAATAATTCAATGA
950442 CCATTTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (30 bp):
TAAAAAAAACTTTCAAATAATTCAATGATT
Found at i:951774 original size:32 final size:31
Alignment explanation
Indices: 951738--951800 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
951728 CTTAACAGTC
*
951738 CAATGACTTAAAACAAAAACTTTCAAATAGTT
1 CAATGACCT-AAACAAAAACTTTCAAATAGTT
** *
951770 CAATGACCTAAATGAAAACTTTCGAATAGTT
1 CAATGACCTAAACAAAAACTTTCAAATAGTT
951801 TAGTGATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
CAATGACCTAAACAAAAACTTTCAAATAGTT
Found at i:953094 original size:40 final size:40
Alignment explanation
Indices: 953034--953174 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 40
953024 AACACACCAG
* *
953034 TTTGGCACCCAGTGCCTCATCGGATAATTCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
* * **
953074 TTTGACACCCAGTGTCTCATCGGTTAAAACTGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATTC-GAAGTAATAA
* * * *
953113 -TTGGCACCCAGTGCCTCATTGAATTAATTCGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAA
* *
953153 TTTGACACTCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
953175 ACTTGAAGTC
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
38 23 0.29
39 6 0.08
40 28 0.36
41 21 0.27
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
Found at i:954075 original size:16 final size:15
Alignment explanation
Indices: 954054--954117 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
954044 TTCTCCTTCC
* *
954054 TTTCTTTCCTTTTTCT
1 TTTCTTTTCTTTCT-T
954070 TTTC-TTTCTTTCTT
1 TTTCTTTTCTTTCTT
*
954084 TTTCTTTTTCTTTCTG
1 TTTC-TTTTCTTTCTT
*
954100 TTTCGTTTCTTTCTT
1 TTTCTTTTCTTTCTT
954115 TTT
1 TTT
954118 ATTTATTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.12
15 19 0.46
16 17 0.41
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:954076 original size:20 final size:20
Alignment explanation
Indices: 954053--954098 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
954043 TTTCTCCTTC
954053 CTTTCTTTCCTTTTTC-TTTT
1 CTTTCTTT-CTTTTTCTTTTT
954073 CTTTCTTTCTTTTTCTTTTT
1 CTTTCTTTCTTTTTCTTTTT
954093 CTTTCT
1 CTTTCT
954099 GTTTCGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
CTTTCTTTCTTTTTCTTTTT
Found at i:956895 original size:27 final size:27
Alignment explanation
Indices: 956857--956912 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
956847 TAGGAGTTTG
956857 ACCCAACTCGATTTTGAATTTAGTGGA
1 ACCCAACTCGATTTTGAATTTAGTGGA
956884 ACCCAACTCGATTTTGAATTTAGTGGA
1 ACCCAACTCGATTTTGAATTTAGTGGA
956911 AC
1 AC
956913 TATGAATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (27 bp):
ACCCAACTCGATTTTGAATTTAGTGGA
Found at i:957056 original size:31 final size:30
Alignment explanation
Indices: 957016--957119 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
957006 ATGAGAATAT
*
957016 TAATGAAAATTTTTAAAAATTTTGGAGGACC
1 TAATTAAAATTTTTAAAAATTTTGGAGG-CC
** * *
957047 TAATTAAAA--TTTAAACCTTTTGAAAGGCT
1 TAATTAAAATTTTTAAAAATTTTG-GAGGCC
* * * *
957076 TAATTAGAATTTCTAAAAATTTTGAGGGGTC
1 TAATTAAAATTTTTAAAAATTTTG-GAGGCC
957107 TAATTAAAATTTT
1 TAATTAAAATTTT
957120 AAATTTTTCT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
29 20 0.36
30 3 0.05
31 32 0.58
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (30 bp):
TAATTAAAATTTTTAAAAATTTTGGAGGCC
Found at i:957059 original size:29 final size:28
Alignment explanation
Indices: 957027--957127 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 28
957017 AATGAAAATT
957027 TTTAAAAATTTTGGAGGACCTAATTAAAA
1 TTTAAAAATTTTGGAGG-CCTAATTAAAA
** * * *
957056 TTTAAACCTTTTGAAAGGCTTAATTAGAAT
1 TTTAAAAATTTTG-GAGGCCTAATTA-AAA
* *
957086 TTCTAAAAATTTTGAGGGGTCTAATTAAAA
1 TT-TAAAAATTTTG-GAGGCCTAATTAAAA
* *
957116 TTTTAAATTTTT
1 TTTAAAAATTTT
957128 CTAAAGCTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 26 0.47
30 11 0.20
31 18 0.33
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.42
Consensus pattern (28 bp):
TTTAAAAATTTTGGAGGCCTAATTAAAA
Found at i:959551 original size:14 final size:14
Alignment explanation
Indices: 959532--959569 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
959522 GTAATTTTAA
959532 TAATTATATATTTG
1 TAATTATATATTTG
959546 TAATTAT-TATTTG
1 TAATTATATATTTG
959559 TAATTA-ATATT
1 TAATTATATATT
959570 AGTTTATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
TAATTATATATTTG
Found at i:962585 original size:20 final size:20
Alignment explanation
Indices: 962560--962623 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
962550 ACCTTGAATA
962560 AGTTCAAGATTTGGGGTTCG
1 AGTTCAAGATTTGGGGTTCG
*
962580 AGTTCATA-ATTT-CGGTTCG
1 AGTTCA-AGATTTGGGGTTCG
* *
962599 AGATTTAAGATTTTGGGTTTCG
1 AG-TTCAAGA-TTTGGGGTTCG
962621 AGT
1 AGT
962624 AAAAAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
19 9 0.26
20 14 0.40
21 5 0.14
22 7 0.20
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (20 bp):
AGTTCAAGATTTGGGGTTCG
Found at i:962984 original size:3 final size:3
Alignment explanation
Indices: 962976--963004 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
962966 ATGTCTTTAA
962976 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
963005 CAATTAAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:965432 original size:16 final size:16
Alignment explanation
Indices: 965407--965437 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
965397 TTTTATCATT
965407 TATTAATATAAAAAGC
1 TATTAATATAAAAAGC
*
965423 TATTATTATAAAAAG
1 TATTAATATAAAAAG
965438 TAAAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
TATTAATATAAAAAGC
Found at i:967848 original size:3 final size:3
Alignment explanation
Indices: 967842--967867 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
967832 TTTATGTTGT
967842 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
967868 TGCTATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:977690 original size:124 final size:124
Alignment explanation
Indices: 977542--977919 Score: 372
Period size: 124 Copynumber: 3.1 Consensus size: 124
977532 CATGCATGTA
* * * * *
977542 AACATACAT-ATATATATATAGTATTTACAGCATTTAGGTGCAAGCAATCTCATATTCTATCAAT
1 AACATACATAATACAGAT-TAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
** * * *
977606 TGAAAGGCAAATCATACATAAGCAACTATGGGACAACTAATTATTCATTGACATAACTGC
65 TCTAAGGCAAATCATAAATAAGCAACTATGGGTCAACTAATCATTCATTGACATAACTGC
*** * * * *
977666 AGTGTTTACAT-ATAC-G-TCTAGTATTTACAACATGTAGATGCAAGAAACCTCATATTTTATCA
1 A--ACATACATAATACAGAT-TAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCA
* * ** * *
977728 ATTCTAAGGTAAATCATAAATCAGCAACTA-GGGTCAACTTGTCATTCATTGGCATAACAGC
63 ATTCTAAGGCAAATCATAAATAAGCAACTATGGGTCAACTAATCATTCATTGACATAACTGC
* * * *
977789 AACATACATACATACAGATT-GTATTTGCAGCATTTAGATGCAATAAAACTCAAATTCTATTAAT
1 AACATACATA-ATACAGATTAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* * * * *
977853 TCTGAGGCAAATAATAAATAAGCATCTATGGGTCAATTAATCATTCAGTGACATAACTGC
65 TCTAAGGCAAATCATAAATAAGCAACTATGGGTCAACTAATCATTCATTGACATAACTGC
*
977913 AATATAC
1 AACATAC
977920 TTGTACAATC
Statistics
Matches: 201, Mismatches: 46, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
121 5 0.02
123 89 0.44
124 98 0.49
125 1 0.00
126 8 0.04
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (124 bp):
AACATACATAATACAGATTAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATT
CTAAGGCAAATCATAAATAAGCAACTATGGGTCAACTAATCATTCATTGACATAACTGC
Found at i:978063 original size:150 final size:150
Alignment explanation
Indices: 977790--978521 Score: 745
Period size: 150 Copynumber: 4.9 Consensus size: 150
977780 CATAACAGCA
* * * * * * *
977790 ACATACATACATACAGATTGTATTTGCAGCATTTAGATGCAATAAAACTCAAATTCTATTAATTC
1 ACATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTC
* * * * * * *
977855 TGAGGCAAATAATAAATAAGCATCTATGGGTCAATTAATCATTCAGTGACATAACTGCAATATAC
66 TAAGGCAAATTATAAAAAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAATATAC
* * * *
977920 TTGTACA-ATCATATATATAT
131 ATATACATA-CATACATACAT
* *
977940 ACATACATACATATAAATAGTATTTACAGCATTTTGATGCAAGAAAACTCGTATTCTATCAATTC
1 ACATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTC
* * *
978005 TAAGGCAAATTATAGAAAACCAACTATGGGTCAACTAACCATTCATTGACATAGCTGCAATATAC
66 TAAGGCAAATTATAAAAAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAATATAC
*
978070 ATATACATGCATACATATC-T
131 ATATACATACATACATA-CAT
* * * *
978090 ACATATC-TACATCCATACATATAGTATTTACAGCATTTATATGCGAGAGAACTCATATTCTGTC
1 ACATA-CATACAT--ATA-A-ATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATC
* * * * *
978154 AGTTCTAAGGCAAATCATAAAAAACCAACTATGGGTCAACTAGTCATTCATTAACATAATTGCAA
61 AATTCTAAGGCAAATTATAAAAAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAA
*
978219 TATACATATAC-T--ATACATGCAT
126 TATACATATACATACATACATACAT
* *
978241 ACATAC--ACATAT--ATAGTATTTCCAGCATTTAGATGCAAGAAATCTCATATTCTATCAATTC
1 ACATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTC
* * * * *
978302 TAAGGCATA-TATAAAGAAACCAACTATGGGTCAACTAATAATTGATTGACAT-ACATACATACA
66 TAAGGCAAATTATAAA-AAACCAACTATGGGTCAACTAATCATTCATTGACATAAC-TGCA-ATA
978365 TACATACATACATACATACATACAT
128 TACAT--ATACATACATACATACAT
* * * * * * *
978390 ACATACATACATACATATACAGTATTCAAAGTATTTAGATGCAATAAAACTCGTATTCTATCAAT
1 ACATACATACAT--ATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAAT
* * * *
978455 TCTAAGGCTAATTATTGAAAAACCAACTAT-GGTCAAGTAATCA-TCAATTGACATAACTACATA
64 TCTAAGGCAAATTA-TAAAAAACCAACTATGGGTCAACTAATCATTC-ATTGACATAACTGCA-A
978518 TATA
126 TATA
978522 GAGAATCTAC
Statistics
Matches: 485, Mismatches: 71, Indels: 47
0.80 0.12 0.08
Matches are distributed among these distances:
142 6 0.01
143 85 0.18
144 7 0.01
146 4 0.01
147 3 0.01
149 19 0.04
150 136 0.28
151 17 0.04
152 3 0.01
153 4 0.01
154 107 0.22
155 76 0.16
156 15 0.03
157 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (150 bp):
ACATACATACATATAAATAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTC
TAAGGCAAATTATAAAAAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAATATAC
ATATACATACATACATACAT
Found at i:978357 original size:4 final size:4
Alignment explanation
Indices: 978350--978406 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
978340 TAATTGATTG
978350 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
978398 ACAT ACAT A
1 ACAT ACAT A
978407 TACAGTATTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:978880 original size:3 final size:3
Alignment explanation
Indices: 978874--978901 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
978864 GGAATAATAA
978874 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
978902 TAATTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:979609 original size:18 final size:20
Alignment explanation
Indices: 979573--979609 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
979563 TAAAATTTTA
*
979573 TATATTATATACATTTATTG
1 TATATTATATACATATATTG
979593 TATATTATA-A-ATATATT
1 TATATTATATACATATATT
979610 TTAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.38
19 1 0.06
20 9 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TATATTATATACATATATTG
Found at i:984221 original size:68 final size:68
Alignment explanation
Indices: 984116--984354 Score: 180
Period size: 68 Copynumber: 3.4 Consensus size: 68
984106 TTCTTCTATC
* *
984116 AATCT-ACCAATTAGTTTATACGAGCTAAATGGTAGTTTAGATAAGATATGAAACATATTTTAAA
1 AATCTAACC-ATTAATTTATACGAGTTAAAT-GTAGTTTAGATAAGATATGAAACATATTTTAAA
*
984180 ATAT-
64 ACATA
* * * * ** * *
984184 GATTTAACCATTAATTTATACGAGTTAAATATCAGTTTA-AAATAGATAAAAAAAAACATATCTA
1 AATCTAACCATTAATTTATACGAGTTAAATGT-AGTTTAGATA-AGAT---ATGAAACATATTTT
984248 AAACACATA
61 AAA-ACATA
* * * * *
984257 AATCTAACCATTAATTTAGACGAGTTAAATGTAAGATTAGATATGAAATGAAGCATATTTTAAAA
1 AATCTAACCATTAATTTATACGAGTTAAATGT-AGTTTAGATAAGATATGAAACATATTTTAAAA
*
984322 CA-C
65 CATA
* * * *
984325 AGTCTAACCATTAGTTTGTACGAGCTAAAT
1 AATCTAACCATTAATTTATACGAGTTAAAT
984355 ACCAATTCTT
Statistics
Matches: 131, Mismatches: 31, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
67 3 0.02
68 57 0.44
69 6 0.05
70 12 0.09
71 13 0.10
72 3 0.02
73 35 0.27
74 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (68 bp):
AATCTAACCATTAATTTATACGAGTTAAATGTAGTTTAGATAAGATATGAAACATATTTTAAAAC
ATA
Found at i:987103 original size:20 final size:22
Alignment explanation
Indices: 987078--987118 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
987068 CAATTGAACC
987078 GAAATTTTAA-AATTT-TTTAG
1 GAAATTTTAATAATTTATTTAG
987098 GAAATTTTAATAATTTATTTA
1 GAAATTTTAATAATTTATTTA
987119 ATCGAGCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
GAAATTTTAATAATTTATTTAG
Found at i:989598 original size:20 final size:20
Alignment explanation
Indices: 989573--989613 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
989563 GTTTTTTAAA
989573 TTTTC-TAGTATTTTATTTCT
1 TTTTCTTAGTATTTT-TTTCT
989593 TTTTCTTAGTATTTTTTTCT
1 TTTTCTTAGTATTTTTTTCT
989613 T
1 T
989614 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTCTTAGTATTTTTTTCT
Found at i:992863 original size:49 final size:49
Alignment explanation
Indices: 992808--992907 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
992798 TCATTAAAAT
992808 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
1 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
*
992857 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCTATAAGTCTTTATAC
1 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
992906 TT
1 TT
992908 CATAAATTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (49 bp):
TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
Found at i:995125 original size:14 final size:14
Alignment explanation
Indices: 995106--995137 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
995096 ATAATTCATG
*
995106 TATATATGTATATA
1 TATATATGCATATA
995120 TATATATGCATATA
1 TATATATGCATATA
995134 TATA
1 TATA
995138 GAATGAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (14 bp):
TATATATGCATATA
Found at i:996775 original size:38 final size:38
Alignment explanation
Indices: 996724--996799 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
996714 TACGACACTT
996724 GAGAATGTTGTACACTATCACTTGAAAATTTAAAATAA
1 GAGAATGTTGTACACTATCACTTGAAAATTTAAAATAA
996762 GAGAATGTTGTACACTATCACTTGAAAATTTAAAATAA
1 GAGAATGTTGTACACTATCACTTGAAAATTTAAAATAA
996800 ATATCAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (38 bp):
GAGAATGTTGTACACTATCACTTGAAAATTTAAAATAA
Found at i:998414 original size:5 final size:5
Alignment explanation
Indices: 998404--998458 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
998394 ATAAAAAAAA
998404 TACCG TACCG TACCG TACCG TACCG TACCG TACCG TACCG TACCG TACCG
1 TACCG TACCG TACCG TACCG TACCG TACCG TACCG TACCG TACCG TACCG
998454 TACCG
1 TACCG
998459 CACTTCCCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
TACCG
Found at i:1003845 original size:16 final size:16
Alignment explanation
Indices: 1003826--1003859 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1003816 GCTTAAAACA
1003826 ACTCGAACTCAAAATG
1 ACTCGAACTCAAAATG
*
1003842 ACTCGAACTTAAAATG
1 ACTCGAACTCAAAATG
1003858 AC
1 AC
1003860 CAAAATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.21
Consensus pattern (16 bp):
ACTCGAACTCAAAATG
Found at i:1008316 original size:84 final size:84
Alignment explanation
Indices: 1008162--1008350 Score: 216
Period size: 84 Copynumber: 2.2 Consensus size: 84
1008152 AATTAGCTGT
* * * * * * * *
1008162 CTTTAAGATGTTTGATAAAATGTTTGTGTTGGGCCAAATCGAGTTGTAGAAGAAATATTAGTGAC
1 CTTTAAGATGTTTGATAATATGTTTATGTTAGACCAAATCAAGTTGTAGAAGAAAAATTAATGAA
*
1008227 CCAAAGTCAAATAAGTTGC
66 CCAAAGACAAATAAGTTGC
* * * *
1008246 CTTTGAGATGTTTGATAATATGTTTATGTTAGACTAATTCAAGTTTTAGAAGAAAAATTAATGAA
1 CTTTAAGATGTTTGATAATATGTTTATGTTAGACCAAATCAAGTTGTAGAAGAAAAATTAATGAA
* * *
1008311 GCAAAGACAAATTAGTTGT
66 CCAAAGACAAATAAGTTGC
* *
1008330 CTTTCAGATGTTTGAGAATAT
1 CTTTAAGATGTTTGATAATAT
1008351 ATTTGTGAAG
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.35
Consensus pattern (84 bp):
CTTTAAGATGTTTGATAATATGTTTATGTTAGACCAAATCAAGTTGTAGAAGAAAAATTAATGAA
CCAAAGACAAATAAGTTGC
Found at i:1028434 original size:15 final size:16
Alignment explanation
Indices: 1028402--1028434 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1028392 AGTGGGAGAA
1028402 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
1028419 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
1028434 T
1 T
1028435 TCCTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:1032144 original size:25 final size:25
Alignment explanation
Indices: 1032098--1032147 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1032088 AAAAAATTCC
1032098 CTATTATTATTATTATTTATTTTTA
1 CTATTATTATTATTATTTATTTTTA
1032123 CTATT-TTATT-TTATTTTCATTTTTA
1 CTATTATTATTATTA-TTT-ATTTTTA
1032148 TTTTTGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
CTATTATTATTATTATTTATTTTTA
Found at i:1032150 original size:6 final size:6
Alignment explanation
Indices: 1032101--1032152 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
1032091 AAATTCCCTA
* *
1032101 TTATTA TTATTAT TTATTT TTACTATT TTA-TT TTATTT TCATTT TTATTT
1 TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT
1032151 TT
1 TT
1032153 GCAGGAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 5 0.13
6 23 0.59
7 6 0.15
8 5 0.13
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:1033333 original size:15 final size:16
Alignment explanation
Indices: 1033301--1033333 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1033291 AGTGGGAGAA
1033301 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
1033318 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
1033333 T
1 T
1033334 TCCTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:1036707 original size:15 final size:15
Alignment explanation
Indices: 1036687--1036767 Score: 51
Period size: 15 Copynumber: 5.4 Consensus size: 15
1036677 TTTATGGAAA
1036687 ATCAAAGATATAGGT
1 ATCAAAGATATAGGT
* *
1036702 ATCAAATA-AT-GGAA
1 ATCAAAGATATAGG-T
*
1036716 AGTCAAAGATATGGGT
1 A-TCAAAGATATAGGT
* **
1036732 ATCAAATAT-TAGAA
1 ATCAAAGATATAGGT
*
1036746 AGTCAAAGATATGGGT
1 A-TCAAAGATATAGGT
1036762 ATCAAA
1 ATCAAA
1036768 TATTGGAAAG
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
13 2 0.04
14 6 0.12
15 32 0.67
16 6 0.12
17 2 0.04
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (15 bp):
ATCAAAGATATAGGT
Found at i:1036716 original size:30 final size:30
Alignment explanation
Indices: 1036680--1036794 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
1036670 ATCCATATTT
* *
1036680 ATGGAAAATCAAAGATATAGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
1036710 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
1036740 TTAGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
1036770 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
1036795 GAGATATTGG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:1036781 original size:15 final size:15
Alignment explanation
Indices: 1036703--1036782 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
1036693 GATATAGGTA
*
1036703 TCAAATAATGGAAAG
1 TCAAATATTGGAAAG
* **
1036718 TCAAAGATATGGGTA-
1 TCAAATAT-TGGAAAG
*
1036733 TCAAATATTAGAAAG
1 TCAAATATTGGAAAG
* **
1036748 TCAAAGATATGGGTA-
1 TCAAATAT-TGGAAAG
1036763 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
1036778 TCAAA
1 TCAAA
1036783 GATATGGGTA
Statistics
Matches: 46, Mismatches: 15, Indels: 8
0.67 0.22 0.12
Matches are distributed among these distances:
14 7 0.15
15 32 0.70
16 7 0.15
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (15 bp):
TCAAATATTGGAAAG
Found at i:1040243 original size:15 final size:15
Alignment explanation
Indices: 1040223--1040330 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
1040213 TTTATGGAAA
1040223 ATCAAATATATGGGT
1 ATCAAATATATGGGT
**
1040238 ATCAAATA-ATGGAA
1 ATCAAATATATGGGT
*
1040252 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
* **
1040268 ATCAAATAT-TAGAA
1 ATCAAATATATGGGT
*
1040282 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
1040298 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
1040312 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
1040328 ATC
1 ATC
1040331 GAGATATTGG
Statistics
Matches: 68, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
14 12 0.18
15 44 0.65
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:1040252 original size:30 final size:30
Alignment explanation
Indices: 1040216--1040330 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
1040206 ATCCATATTT
* *
1040216 ATGGAAAATCAAATATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
1040246 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
1040276 TTAGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
1040306 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
1040331 GAGATATTGG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:1048418 original size:2 final size:2
Alignment explanation
Indices: 1048411--1048447 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1048401 AAGTAGGATA
1048411 TG TG TG TG TG TG 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 TG TG TG TG TG TG T
1048448 ATAGGTCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1051570 original size:2 final size:2
Alignment explanation
Indices: 1051563--1051587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1051553 TGGCTAACCA
1051563 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 T
1051588 ATATATATAT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1059538 original size:29 final size:29
Alignment explanation
Indices: 1059492--1059551 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1059482 TGTTCATTTC
1059492 TTAAACCCCCCACAAGGTGGGTTTTGGGG
1 TTAAACCCCCCACAAGGTGGGTTTTGGGG
*
1059521 TTAAACCCCCCACGAGGTGGGTTTTGGGG
1 TTAAACCCCCCACAAGGTGGGTTTTGGGG
1059550 TT
1 TT
1059552 TTAGCCCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (29 bp):
TTAAACCCCCCACAAGGTGGGTTTTGGGG
Found at i:1061838 original size:30 final size:30
Alignment explanation
Indices: 1061799--1061874 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
1061789 GAAGGAATAG
*
1061799 AATATAATTTTATTATTTTTAAAAGATTTA
1 AATATAATTTTATTATTTTTAAAAGATTAA
* *
1061829 AATACAATTTTTTTATTTTTAAAAGATTAA
1 AATATAATTTTATTATTTTTAAAAGATTAA
*
1061859 AATGTAATTTTATTAT
1 AATATAATTTTATTAT
1061875 ACATTCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
AATATAATTTTATTATTTTTAAAAGATTAA
Found at i:1069017 original size:43 final size:43
Alignment explanation
Indices: 1068951--1069076 Score: 150
Period size: 43 Copynumber: 2.9 Consensus size: 43
1068941 ATAGGATTTC
* *
1068951 CGATATGTGTTCTCATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATCTGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCAT
*
1068994 CGA-CTTGTGTTTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATC-TGTGTTTTCATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* * *
1069037 CGATCTGTATTTACATGTAAGACCACGTCTAGGACGTTGG
1 CGATCTGTGTTTTCATGTAAGACCACGTCTGGGACGTTGG
1069077 TATTGTACAA
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 65 0.93
44 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (43 bp):
CGATCTGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:1071596 original size:16 final size:16
Alignment explanation
Indices: 1071575--1071606 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1071565 ACTTTCATAT
1071575 AATATTGCCACATTCA
1 AATATTGCCACATTCA
1071591 AATATTGCCACATTCA
1 AATATTGCCACATTCA
1071607 TATAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (16 bp):
AATATTGCCACATTCA
Found at i:1074717 original size:18 final size:18
Alignment explanation
Indices: 1074690--1074782 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
1074680 TACGACCGTT
1074690 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
1074708 TACGGCACTATTCATGTA
1 TACGGTACTATTCACGTA
*
1074726 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
* *
1074744 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
1074762 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
1074780 TAC
1 TAC
1074783 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:1074737 original size:36 final size:36
Alignment explanation
Indices: 1074690--1074782 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
1074680 TACGACCGTT
*
1074690 TACGGTACTATTCACGTATACGGCACTATTCATGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
* *
1074726 TACGGTACTATTTACGTATATGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
1074762 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
1074783 AGTAGTTGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:1084866 original size:18 final size:18
Alignment explanation
Indices: 1084837--1084929 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
1084827 TACGACCGTT
* *
1084837 TACGGTACTATTCACATA
1 TACGGCACTATTCACGTA
*
1084855 TACAGCACTATTCACGTA
1 TACGGCACTATTCACGTA
*
1084873 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
1084891 TACGGCACTATTTACATA
1 TACGGCACTATTCACGTA
*
1084909 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
1084927 TAC
1 TAC
1084930 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:1084884 original size:36 final size:36
Alignment explanation
Indices: 1084837--1084931 Score: 154
Period size: 36 Copynumber: 2.6 Consensus size: 36
1084827 TACGACCGTT
* *
1084837 TACGGTACTATTCACATATACAGCACTATTCACGTA
1 TACGGTACTATTCACGTATACAGCACTATTCACATA
* *
1084873 TACGGTACTATTCACGTATACGGCACTATTTACATA
1 TACGGTACTATTCACGTATACAGCACTATTCACATA
1084909 TACGGTACTATTCACGTATACAG
1 TACGGTACTATTCACGTATACAG
1084932 TAGTTGGGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACAGCACTATTCACATA
Found at i:1090846 original size:19 final size:20
Alignment explanation
Indices: 1090799--1090846 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1090789 TACATAAAAA
*
1090799 ATGATAATAATAATAAAAGT
1 ATGATAATATTAATAAAAGT
* *
1090819 ATAAT-ATATTAAT-AAATT
1 ATGATAATATTAATAAAAGT
1090837 ATGATAATAT
1 ATGATAATAT
1090847 GAAAATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
ATGATAATATTAATAAAAGT
Found at i:1092811 original size:8 final size:8
Alignment explanation
Indices: 1092798--1092884 Score: 72
Period size: 8 Copynumber: 10.5 Consensus size: 8
1092788 TGTTAAAAAA
1092798 ATATTATT
1 ATATTATT
1092806 ATATTA-T
1 ATATTATT
*
1092813 AGTAATGATT
1 A-T-ATTATT
* *
1092823 ATGTTTTT
1 ATATTATT
1092831 ATATTA-T
1 ATATTATT
1092838 ATTATTATT
1 A-TATTATT
1092847 A-ATATATT
1 ATAT-TATT
1092855 ATATTATATT
1 ATA-T-TATT
1092865 ATATTATT
1 ATATTATT
1092873 ATATTATT
1 ATATTATT
1092881 ATAT
1 ATAT
1092885 ATATATGACA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
7 6 0.09
8 40 0.62
9 8 0.12
10 11 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
ATATTATT
Found at i:1092812 original size:5 final size:5
Alignment explanation
Indices: 1092802--1092890 Score: 71
Period size: 5 Copynumber: 17.6 Consensus size: 5
1092792 AAAAAAATAT
* *
1092802 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
1092848 -A-TA TATTA TATTA TATTA TATTA T-TATA TTATTA TATATA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT-TA -TATTA TAT-TA TAT
1092891 GACAAAGAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 21
0.74 0.03 0.22
Matches are distributed among these distances:
3 4 0.06
4 5 0.07
5 40 0.57
6 19 0.27
7 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:1092845 original size:3 final size:3
Alignment explanation
Indices: 1092832--1092882 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
1092822 TATGTTTTTA
*
1092832 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1092874 TAT TAT TAT
1 TAT TAT TAT
1092883 ATATATATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
2 12 0.29
3 29 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Done.