Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 30 of 31
Found at i:5796066 original size:21 final size:20
Alignment explanation
Indices: 5796036--5796077 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
5796026 ATATTTATTT
5796036 AAAATTAAAATTATT-TTTAA
1 AAAATTAAAATT-TTATTTAA
5796056 AAAATTTAAAATTTTATTTAA
1 AAAA-TTAAAATTTTATTTAA
5796077 A
1 A
5796078 TCAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTAAAATTTTATTTAA
Found at i:5796704 original size:21 final size:22
Alignment explanation
Indices: 5796680--5796721 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5796670 TTTAAAATTA
*
5796680 AATATATTA-AATATTATTTTT
1 AATATAATATAATATTATTTTT
5796701 AATATAATATAATATTATTTT
1 AATATAATATAATATTATTTT
5796722 ATTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATAATATAATATTATTTTT
Found at i:5796756 original size:21 final size:21
Alignment explanation
Indices: 5796732--5796815 Score: 55
Period size: 25 Copynumber: 3.8 Consensus size: 21
5796722 ATTTTAATTT
5796732 TTAATTAATATTTTATTTAAA
1 TTAATTAATATTTTATTTAAA
*
5796753 TTAATCTTTATTTATTTTATTTAAA
1 TTAA---TTA-ATATTTTATTTAAA
* *
5796778 TT--TTAATATATTTATATAATT
1 TTAATTAATAT-TTTATTTAA-A
*
5796799 TTATATTAATTTTTTAT
1 TTA-ATTAATATTTTAT
5796816 ATCATATAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
19 3 0.06
20 11 0.22
21 6 0.12
23 5 0.10
24 9 0.18
25 15 0.31
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAATTAATATTTTATTTAAA
Found at i:5805616 original size:24 final size:25
Alignment explanation
Indices: 5805579--5805626 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5805569 AATATTAAAA
* *
5805579 TTATATATTTAATATTT-AATTTAT
1 TTATAAATTAAATATTTCAATTTAT
5805603 TTATAAATTAAATATTTCAATTTA
1 TTATAAATTAAATATTTCAATTTA
5805627 ATTGATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATAAATTAAATATTTCAATTTAT
Found at i:5808375 original size:174 final size:174
Alignment explanation
Indices: 5808078--5808423 Score: 523
Period size: 174 Copynumber: 2.0 Consensus size: 174
5808068 CGTTACTGTT
* * ** * *
5808078 TAAAGTGCTCTCCAATGTGCCAACCACCGAAATGTTATCCACATTTGTGCCAACAGTTGATATCA
1 TAAAGTACTCTCCAATGTGCCAACCACCGAAATGTTAGCCACATTTACGCCAACAGTTAAAATCA
* *
5808143 AACCGTCTAATCCAAAGGAAGAGCTACAATCACGTTCGAGTCCAATCTCATCACCTTGATCATCA
66 AACCATCTAATCCAAAGGAAGAGCTACAATCACGTTCAAGTCCAATCTCATCACCTTGATCATCA
5808208 AGATCATCAAAGTTCTCAGTTCCCACAGATGCAGGTGCATTTAA
131 AGATCATCAAAGTTCTCAGTTCCCACAGATGCAGGTGCATTTAA
* * * *
5808252 TAAAGTACTCTCCAATGTGCCAACCTCTGAAATGTTAGCCACTTTTACGCCAACGGTTAAAATCA
1 TAAAGTACTCTCCAATGTGCCAACCACCGAAATGTTAGCCACATTTACGCCAACAGTTAAAATCA
* * *
5808317 AACCATCTAATCCAAGGGAAGAGCTACAATCACGTTCAATTCCAA-CTTCATCACCTTGATCATT
66 AACCATCTAATCCAAAGGAAGAGCTACAATCACGTTCAAGTCCAATC-TCATCACCTTGATCATC
* *
5808381 AAGATCATCATAGTTTTCAGTTCCCACAGATGCAGGTGCATTT
130 AAGATCATCAAAGTTCTCAGTTCCCACAGATGCAGGTGCATTT
5808424 GAAATCTCTT
Statistics
Matches: 154, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
173 1 0.01
174 153 0.99
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (174 bp):
TAAAGTACTCTCCAATGTGCCAACCACCGAAATGTTAGCCACATTTACGCCAACAGTTAAAATCA
AACCATCTAATCCAAAGGAAGAGCTACAATCACGTTCAAGTCCAATCTCATCACCTTGATCATCA
AGATCATCAAAGTTCTCAGTTCCCACAGATGCAGGTGCATTTAA
Found at i:5816405 original size:15 final size:16
Alignment explanation
Indices: 5816385--5816421 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
5816375 GAAAAGAATT
5816385 AAAAATATAATT-TAA
1 AAAAATATAATTATAA
*
5816400 AAAAATATATTTATAA
1 AAAAATATAATTATAA
5816416 AAAAAT
1 AAAAAT
5816422 TATTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATATAATTATAA
Found at i:5818308 original size:20 final size:21
Alignment explanation
Indices: 5818285--5818336 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5818275 CATGATAATA
*
5818285 TATCGATACAT-AT-TGCAATG
1 TATCGATACATCATGTG-AAAG
*
5818305 TATCGATGCATCATGTGAAAG
1 TATCGATACATCATGTGAAAG
5818326 TATCGATACAT
1 TATCGATACAT
5818337 TTCAATGGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.37
21 15 0.56
22 2 0.07
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
TATCGATACATCATGTGAAAG
Found at i:5819175 original size:3 final size:3
Alignment explanation
Indices: 5819167--5819211 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
5819157 TCACTCAAAG
* * * *
5819167 TGA TGA TGA TGA TGA TGA TGA TCA TGA TCA TGA TCA TGA TCA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
5819212 GGTTGAGGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:5819178 original size:6 final size:6
Alignment explanation
Indices: 5819167--5819211 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
5819157 TCACTCAAAG
* * *
5819167 TGATGA TGATGA TGATGA TGATCA TGATCA TGATCA TGATCA TGA
1 TGATCA TGATCA TGATCA TGATCA TGATCA TGATCA TGATCA TGA
5819212 GGTTGAGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (6 bp):
TGATCA
Found at i:5826090 original size:20 final size:20
Alignment explanation
Indices: 5826065--5826136 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
5826055 CCCTTATTTC
5826065 TATCGATACATATAAAAATG
1 TATCGATACATATAAAAATG
* *
5826085 TATCGATACATATTACAATG
1 TATCGATACATATAAAAATG
***
5826105 TATCGATACATTATGTGAATG
1 TATCGATACA-TATAAAAATG
5826126 TATCGATACAT
1 TATCGATACAT
5826137 TTCATTGGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATATAAAAATG
Found at i:5827524 original size:21 final size:21
Alignment explanation
Indices: 5827498--5827539 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5827488 AAAAAGTAAA
5827498 AAAAAATGAA-AATTTAGAAAG
1 AAAAAAT-AATAATTTAGAAAG
5827519 AAAAAATAATAATTTAGAAAG
1 AAAAAATAATAATTTAGAAAG
5827540 TTCATCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (21 bp):
AAAAAATAATAATTTAGAAAG
Found at i:5828913 original size:45 final size:44
Alignment explanation
Indices: 5828848--5828932 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
5828838 ATATAAATAT
** *
5828848 ATATTTTAAAATTTTTATAATATTA-AAATTTATATAAATAAAAA
1 ATATTTTAAAATAATTATAATATTATAAA-ATATATAAATAAAAA
5828892 ATATTTTAAATATAATTATAATATTATAAAATATATAAATA
1 ATATTTTAAA-ATAATTATAATATTATAAAATATATAAATA
5828933 CATTATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 10 0.28
45 23 0.64
46 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (44 bp):
ATATTTTAAAATAATTATAATATTATAAAATATATAAATAAAAA
Found at i:5829665 original size:3 final size:3
Alignment explanation
Indices: 5829657--5829709 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
5829647 TTTGAAGATG
5829657 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5829705 ATA AT
1 ATA AT
5829710 TCTCCTAGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5832027 original size:16 final size:16
Alignment explanation
Indices: 5831993--5832056 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
5831983 TAACATAAAT
5831993 TTAATAATATTAAATATAA
1 TTAATAATA-T-AA-ATAA
5832012 TTAATAATATAAATAA
1 TTAATAATATAAATAA
*
5832028 --AATAAT-TAAAAAA
1 TTAATAATATAAATAA
*
5832041 TAAAATAATATAAATA
1 T-TAATAATATAAATA
5832057 TATATTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 6 0.15
14 6 0.15
16 10 0.26
17 7 0.18
18 1 0.03
19 9 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAATAATATAAATAA
Found at i:5832034 original size:21 final size:21
Alignment explanation
Indices: 5832003--5832053 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5831993 TTAATAATAT
*
5832003 TAAATATAATT-AATAATATAAA
1 TAAA-ATAATTAAAAAATA-AAA
5832025 TAAAATAATTAAAAAATAAAA
1 TAAAATAATTAAAAAATAAAA
*
5832046 TAATATAA
1 TAAAATAA
5832054 ATATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATAATTAAAAAATAAAA
Found at i:5832311 original size:22 final size:22
Alignment explanation
Indices: 5832280--5832346 Score: 62
Period size: 28 Copynumber: 2.7 Consensus size: 22
5832270 TAAAGGTATG
5832280 ATTTAATTTTTAAAAATTTTTAT
1 ATTT-ATTTTTAAAAATTTTTAT
5832303 ATTTATTTTTAGATAATTATATTTTTAT
1 ATTTATTTTT--A-AA--A-ATTTTTAT
*
5832331 ATTTATATTTAAAAAT
1 ATTTATTTTTAAAAAT
5832347 ATATTAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
22 8 0.22
23 5 0.14
24 1 0.03
25 4 0.11
26 1 0.03
27 1 0.03
28 17 0.46
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (22 bp):
ATTTATTTTTAAAAATTTTTAT
Found at i:5832336 original size:14 final size:14
Alignment explanation
Indices: 5832295--5832340 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
5832285 ATTTTTAAAA
5832295 ATTTTTATATTTAT
1 ATTTTTATATTTAT
* *
5832309 -TTTTAGATAATTAT
1 ATTTT-TATATTTAT
5832323 ATTTTTATATTTAT
1 ATTTTTATATTTAT
5832337 ATTT
1 ATTT
5832341 AAAAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.15
14 18 0.69
15 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTTTTATATTTAT
Found at i:5832812 original size:31 final size:31
Alignment explanation
Indices: 5832762--5832821 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
5832752 TATTTTTTAA
*
5832762 AATTAATTATTTTTAATTTA-TTTTAAAAAC
1 AATTAATTATTTTTAATTTACTTATAAAAAC
5832792 AATT-ATTATTCTATTAATTTACTTATAAAA
1 AATTAATTATT-T-TTAATTTACTTATAAAA
5832822 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 8 0.31
32 7 0.27
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (31 bp):
AATTAATTATTTTTAATTTACTTATAAAAAC
Found at i:5833489 original size:21 final size:21
Alignment explanation
Indices: 5833464--5833513 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
5833454 TTAAAGTATA
5833464 TATATATATATTAT-TTTTTAT
1 TATATATAT-TTATATTTTTAT
*
5833485 TATAT-TATTTTTATTTTTAT
1 TATATATATTTATATTTTTAT
*
5833505 TAAATATAT
1 TATATATAT
5833514 CATATTCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATATATATTTATATTTTTAT
Found at i:5835255 original size:2 final size:2
Alignment explanation
Indices: 5835250--5835315 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
5835240 TATATATATG
5835250 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5835292 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
5835316 CTTAACCCGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5835842 original size:27 final size:28
Alignment explanation
Indices: 5835812--5835869 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
5835802 AAATATTAAA
5835812 AAAATAATTTCGT-AAATAA-TTTTTTAT
1 AAAATAATTT-GTAAAATAATTTTTTTAT
* *
5835839 AAAATACTTTTTAAAATAATTTTTTTAT
1 AAAATAATTTGTAAAATAATTTTTTTAT
5835867 AAA
1 AAA
5835870 TATATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 15 0.56
28 11 0.41
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (28 bp):
AAAATAATTTGTAAAATAATTTTTTTAT
Found at i:5835870 original size:15 final size:15
Alignment explanation
Indices: 5835824--5835871 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
5835814 AATAATTTCG
5835824 TAAATAA-TTTTTTA
1 TAAATAATTTTTTTA
*
5835838 T-AA-AATACTTTTTA
1 TAAATAAT-TTTTTTA
5835852 -AAATAATTTTTTTA
1 TAAATAATTTTTTTA
5835866 TAAATA
1 TAAATA
5835872 TATTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 15 0.56
15 8 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATAATTTTTTTA
Found at i:5835881 original size:27 final size:26
Alignment explanation
Indices: 5835825--5835882 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
5835815 ATAATTTCGT
**
5835825 AAATAATTTTTTATAAAATACTTTTTA
1 AAATAATTTTTTATAAAATAC-TTAAA
5835852 AAATAATTTTTTTATAAATATA-TTAAA
1 AAATAA-TTTTTTATAAA-ATACTTAAA
5835879 AAAT
1 AAAT
5835883 CATCATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 13 0.48
28 11 0.41
29 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATAATTTTTTATAAAATACTTAAA
Found at i:5840265 original size:129 final size:122
Alignment explanation
Indices: 5840098--5840440 Score: 412
Period size: 129 Copynumber: 2.8 Consensus size: 122
5840088 ATTAATAAAA
*
5840098 TTTTAATTTAAAATTTTTTGTTTTA-AAAAACATAATAATTAATATTTTAATTTATTAATGTAAA
1 TTTTAATTT--AATTTTTTATTTTATAAAAACATAATAATTAATATTTTAATTTATTAATGTAAA
**** *
5840162 TTTTTTAAACTTAATTAAATATTTTTTTATTTTATTAAAAATTATAATAAAAAACTTTTTATT
64 TTTTTTAAACTTAATTAAATATTTTTTTATTTTATTAAAAA--ATAAT-AAAAA-TAAACACT
* * *
5840225 TTTTATTTTAATTTTTTTAATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATATAA
1 TTTTAATTTAA-TTTTTT-A-TTTTATAAAAACATAATAATTAATATTTTAATTTATTAATGTAA
* * *
5840290 TTTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAAATATAAACCCT
63 ATTTTTTAAACTTAATTAAATATT-TTTTT-ATTTTATTAAAAAATAATAAAAATAAACACT
5840352 TTTTAATTTAATTTTTTA-TTT-T--AAA-A-AATAATTAATATTTTAATTTATTAATGTAAATT
1 TTTTAATTTAATTTTTTATTTTATAAAAACATAATAATTAATATTTTAATTTATTAATGTAAA-T
*
5840411 TTTTTAAAGTTAATTAAATATTTTTTTATT
65 TTTTTAAACTTAATTAAATATTTTTTTATT
5840441 AAAAATAATA
Statistics
Matches: 192, Mismatches: 17, Indels: 24
0.82 0.07 0.10
Matches are distributed among these distances:
117 3 0.02
118 33 0.17
119 23 0.12
120 3 0.02
122 1 0.01
123 3 0.02
125 3 0.02
126 12 0.06
127 20 0.10
128 9 0.05
129 64 0.33
130 5 0.03
131 13 0.07
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (122 bp):
TTTTAATTTAATTTTTTATTTTATAAAAACATAATAATTAATATTTTAATTTATTAATGTAAATT
TTTTAAACTTAATTAAATATTTTTTTATTTTATTAAAAAATAATAAAAATAAACACT
Found at i:5840608 original size:26 final size:26
Alignment explanation
Indices: 5840579--5840651 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 26
5840569 ATTAATATTT
*
5840579 TAAATTT-ATATATAATAAAATAAAAA
1 TAAATTTCATA-AAAATAAAATAAAAA
*
5840605 TAAATTTCATAAAAAT-AAAT-TAAA
1 TAAATTTCATAAAAATAAAATAAAAA
*
5840629 TTAATTT--TAAAAATAAAAATAAA
1 TAAATTTCATAAAAAT-AAAATAAA
5840652 TTAGATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 7 0.18
24 13 0.33
25 5 0.13
26 11 0.28
27 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAATTTCATAAAAATAAAATAAAAA
Found at i:5840634 original size:24 final size:23
Alignment explanation
Indices: 5840614--5840663 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5840604 ATAAATTTCA
*
5840614 TAAAAAT-AAATTAAATTAATTT
1 TAAAAATAAAAATAAATTAATTT
5840636 TAAAAATAAAAATAAATTAGATTT
1 TAAAAATAAAAATAAATTA-ATTT
5840660 TAAA
1 TAAA
5840664 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAAATAAAAATAAATTAATTT
Found at i:5841198 original size:17 final size:17
Alignment explanation
Indices: 5841163--5841211 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5841153 AGTTAACTTT
*
5841163 TAATTATATGAAT-TAAA
1 TAATTATATAAATAT-AA
5841180 TAATTATATAAATATAA
1 TAATTATATAAATATAA
5841197 T-A-TATATAAA-ATAA
1 TAATTATATAAATATAA
5841211 T
1 T
5841212 TAAAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 5 0.17
15 8 0.27
16 1 0.03
17 15 0.50
18 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TAATTATATAAATATAA
Found at i:5841253 original size:33 final size:30
Alignment explanation
Indices: 5841215--5841291 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 30
5841205 AAATAATTAA
5841215 AATATAATATAGTATGAAATATATTTTAAAATT
1 AATATAATATAGTATG-AATATA--TTAAAATT
* *
5841248 TATATAATATAAATTATGAATATATTAAAATT
1 AATATAATAT--AGTATGAATATATTAAAATT
5841280 AATATAAATATA
1 AATAT-AATATA
5841292 AAATATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 1 0.03
32 12 0.32
33 14 0.37
34 6 0.16
35 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (30 bp):
AATATAATATAGTATGAATATATTAAAATT
Found at i:5841257 original size:38 final size:33
Alignment explanation
Indices: 5841185--5841293 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 33
5841175 TTAAATAATT
5841185 ATATAAA-TAT-AATATATATAAAA-TAAT-TAAA
1 ATATAAATTATGAATATAT-TAAAATTAATAT-AA
*
5841216 ATATAATATAGTATGAAATATATTTTAAAATTTATAT-A
1 ATATAA-AT--TATG-AATATA--TTAAAATTAATATAA
5841254 ATATAAATTATGAATATATTAAAATTAATATAA
1 ATATAAATTATGAATATATTAAAATTAATATAA
5841287 ATATAAA
1 ATATAAA
5841294 ATATTTTAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
31 6 0.09
32 13 0.20
33 8 0.12
34 6 0.09
35 7 0.11
37 8 0.12
38 12 0.18
39 4 0.06
40 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (33 bp):
ATATAAATTATGAATATATTAAAATTAATATAA
Found at i:5841260 original size:16 final size:15
Alignment explanation
Indices: 5841241--5841308 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 15
5841231 AAATATATTT
5841241 TAAAATTTATATAATA
1 TAAAATTTATA-AATA
5841257 T-AAA-TTATGAATATA
1 TAAAATTTAT-AA-ATA
5841272 TTAAAATTAATATAAATA
1 -TAAAATT--TATAAATA
*
5841290 TAAAATATTTTAAATA
1 TAAAAT-TTATAAATA
5841306 TAA
1 TAA
5841309 TTATAATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
14 5 0.12
15 7 0.16
16 12 0.28
17 9 0.21
18 5 0.12
19 2 0.05
20 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (15 bp):
TAAAATTTATAAATA
Found at i:5841296 original size:27 final size:27
Alignment explanation
Indices: 5841200--5841351 Score: 91
Period size: 32 Copynumber: 5.3 Consensus size: 27
5841190 AATATAATAT
5841200 ATATAAAATA-ATTAAAATATAATAT-A
1 ATATAAAATATATTAAAAT-TAATATAA
* * *
5841226 GTATGAAATATATTTTAAAATTTATATAA
1 ATAT-AAA-ATATATTAAAATTAATATAA
*
5841255 TATAAATTATGAATATATTAAAATTAATATAA
1 -AT--A-TA-AAATATATTAAAATTAATATAA
*
5841287 ATATAAAATAT-TTTAAATATAATTATAA
1 ATATAAAATATATTAAAAT-TAA-TATAA
5841315 TATAATAAAATATA--AAACA-TAATATAA
1 -AT-ATAAAATATATTAAA-ATTAATATAA
5841342 ATATATAAAT
1 ATATA-AAAT
5841352 TGTGAAGTAA
Statistics
Matches: 100, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
25 3 0.03
26 15 0.15
27 16 0.16
28 18 0.18
29 13 0.13
30 11 0.11
31 2 0.02
32 20 0.20
33 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATAAAATATATTAAAATTAATATAA
Found at i:5841316 original size:60 final size:59
Alignment explanation
Indices: 5841185--5841341 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 59
5841175 TTAAATAATT
* * *
5841185 ATATAAATATAATATATATAAAATAATTAAAATATAATATAGTATGAAATATATTTTAA
1 ATATAATTATAATATAAATAAAATAATTAAAATATAATATAATATGAAATATATTTTAA
* *
5841244 A-AT-TTATATAATATAAATTATGAATATATTAAAAT-TAATATAAATAT-AAA-ATATTTTAA
1 ATATAAT-TATAATATAAA-TA-AAATA-ATTAAAATATAATAT-AATATGAAATATATTTTAA
*
5841303 ATATAATTATAATAT-AATAAAAT-A-TAAAACATAATATAA
1 ATATAATTATAATATAAATAAAATAATTAAAATATAATATAA
5841342 ATATATAAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
54 7 0.09
55 7 0.09
57 3 0.04
58 14 0.17
59 15 0.18
60 23 0.28
61 13 0.16
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (59 bp):
ATATAATTATAATATAAATAAAATAATTAAAATATAATATAATATGAAATATATTTTAA
Found at i:5849578 original size:18 final size:19
Alignment explanation
Indices: 5849539--5849580 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5849529 ATGTTATATA
* *
5849539 AATAATTAAAATTTACATT
1 AATATTTAAAATTTAAATT
5849558 AATATTTAAAA-TTAAATT
1 AATATTTAAAATTTAAATT
5849576 AATAT
1 AATAT
5849581 AATTTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTTAAAATTTAAATT
Found at i:5849798 original size:22 final size:22
Alignment explanation
Indices: 5849758--5849804 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5849748 ACTAAATCTT
* * * *
5849758 TAAATATTATAATTTTTATTTA
1 TAAATATAATAAATCTTATTAA
5849780 TAAATATAATAAATCTTATTAA
1 TAAATATAATAAATCTTATTAA
5849802 TAA
1 TAA
5849805 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAATATAATAAATCTTATTAA
Found at i:5850348 original size:20 final size:20
Alignment explanation
Indices: 5850323--5850370 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
5850313 TTATCAAATC
*
5850323 ATAAAATTGATTAAAATTTA
1 ATAAAATCGATTAAAATTTA
5850343 ATAAAATCGATTAAAATTTA
1 ATAAAATCGATTAAAATTTA
5850363 ATAAAATC
1 ATAAAATC
5850371 ATAAATCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
ATAAAATCGATTAAAATTTA
Found at i:5850589 original size:16 final size:16
Alignment explanation
Indices: 5850568--5850598 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5850558 TCTAATAGTA
5850568 AATAAATATTAAATAT
1 AATAAATATTAAATAT
*
5850584 AATAAATATTTAATA
1 AATAAATATTAAATA
5850599 AGAATGTGAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:5851743 original size:23 final size:22
Alignment explanation
Indices: 5851711--5851753 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5851701 AATTTTTATT
*
5851711 TAAATTTAATTTTAAAAATATA
1 TAAATTTAATATTAAAAATATA
5851733 TAAATATTAATATTAAAAATA
1 TAAAT-TTAATATTAAAAATA
5851754 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTAATATTAAAAATATA
Found at i:5853065 original size:24 final size:23
Alignment explanation
Indices: 5853011--5853065 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5853001 TAAAAAATTA
* *
5853011 AATATTAAATATTTAATTTTAAT
1 AATAATAAATATTAAATTTTAAT
*
5853034 AGTAAATAAATATTAAATATTTAAT
1 AAT-AATAAATATTAAAT-TTTAAT
5853059 AATAATA
1 AATAATA
5853066 TAAATTTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 16 0.62
25 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATAATAAATATTAAATTTTAAT
Found at i:5853065 original size:31 final size:30
Alignment explanation
Indices: 5853009--5853070 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
5852999 AATAAAAAAT
**
5853009 TAAATATTAAATATTTAATTTTAATAGTAAA
1 TAAATATTAAATATTTAATAATAATA-TAAA
5853040 TAAATATTAAATATTTAATAATAATATAAA
1 TAAATATTAAATATTTAATAATAATATAAA
5853070 T
1 T
5853071 TTGATTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
TAAATATTAAATATTTAATAATAATATAAA
Found at i:5853520 original size:2 final size:2
Alignment explanation
Indices: 5853513--5853540 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5853503 GTCATACTAA
5853513 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
5853541 CATTGATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5854242 original size:23 final size:22
Alignment explanation
Indices: 5854210--5854253 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
5854200 ATTTTTTATT
*
5854210 TAAATTTAATTTTAAAAATATA
1 TAAATTTAATATTAAAAATATA
5854232 TAAATATTAATATTAAAAATAT
1 TAAAT-TTAATATTAAAAATAT
5854254 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTTAATATTAAAAATATA
Found at i:5855343 original size:20 final size:18
Alignment explanation
Indices: 5855306--5855345 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
5855296 TCGTGTCATA
5855306 AACATGTAAAACACGTAT
1 AACATGTAAAACACGTAT
*
5855324 AACATGTATATAACATGTAT
1 AACATGTA-A-AACACGTAT
5855344 AA
1 AA
5855346 GACACGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (18 bp):
AACATGTAAAACACGTAT
Found at i:5857003 original size:16 final size:15
Alignment explanation
Indices: 5856982--5857063 Score: 67
Period size: 16 Copynumber: 5.2 Consensus size: 15
5856972 TTTTACAAAT
5856982 ATATGTTAAATTAAAA
1 ATATGTTAAA-TAAAA
5856998 ATATGTTAAATAAAA
1 ATATGTTAAATAAAA
* *
5857013 GATCATG-AAAATAAAT
1 -AT-ATGTTAAATAAAA
* *
5857029 ATCATATTACATAAAA
1 AT-ATGTTAAATAAAA
*
5857045 ATATATTAAATTAAAA
1 ATATGTTAAA-TAAAA
5857061 ATA
1 ATA
5857064 ATTGTATTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
15 17 0.31
16 35 0.64
17 3 0.05
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.33
Consensus pattern (15 bp):
ATATGTTAAATAAAA
Found at i:5857862 original size:22 final size:22
Alignment explanation
Indices: 5857837--5857885 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
5857827 ACTAAATCTT
* *
5857837 TAAATATTACAATTTTTATTAA
1 TAAATATGACAAATTTTATTAA
* *
5857859 TAAATGTGATAAATTTTATTAA
1 TAAATATGACAAATTTTATTAA
5857881 -AAATA
1 TAAATA
5857886 AAAAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TAAATATGACAAATTTTATTAA
Found at i:5857901 original size:17 final size:18
Alignment explanation
Indices: 5857869--5857903 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
5857859 TAAATGTGAT
5857869 AAATTTTATTAAAAATAAA
1 AAATTTTA-TAAAAATAAA
5857888 AAATTTTA-AAAAATAA
1 AAATTTTATAAAAATAA
5857904 TAATATGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTTATAAAAATAAA
Found at i:5857989 original size:2 final size:2
Alignment explanation
Indices: 5857965--5858029 Score: 59
Period size: 2 Copynumber: 35.0 Consensus size: 2
5857955 ATTTGTATTT
* *
5857965 TA TA CA TA T- TA T- TA TA TA CA TA TA TA T- TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5858002 TA TA CA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5858030 GAAACTAAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
1 5 0.10
2 47 0.90
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5858627 original size:17 final size:17
Alignment explanation
Indices: 5858607--5858646 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
5858597 CATTTTAATA
5858607 ATAAATAAATATTAAAT
1 ATAAATAAATATTAAAT
*
5858624 AT-AATAAATATTTAAT
1 ATAAATAAATATTAAAT
*
5858640 AGAAATA
1 ATAAATA
5858647 TGAATTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAAATAAATATTAAAT
Found at i:5861134 original size:16 final size:18
Alignment explanation
Indices: 5861094--5861134 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
5861084 AATATTTAAT
5861094 TTTAATAGTAAATAAATA
1 TTTAATAGTAAATAAATA
**
5861112 TCAAATA-T-AATAAATA
1 TTTAATAGTAAATAAATA
5861128 TTTAATA
1 TTTAATA
5861135 AGAATATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
16 13 0.68
17 1 0.05
18 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TTTAATAGTAAATAAATA
Found at i:5862282 original size:23 final size:22
Alignment explanation
Indices: 5862250--5862292 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
5862240 ATTTTTTATT
5862250 TAAATTTAAT-TCTAAAAATATA
1 TAAATTTAATAT-TAAAAATATA
5862272 TAAATATTAATATTAAAAATA
1 TAAAT-TTAATATTAAAAATA
5862293 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 13 0.68
24 1 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATATTAAAAATATA
Found at i:5862885 original size:16 final size:16
Alignment explanation
Indices: 5862864--5862896 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5862854 TAGGTGGCGA
5862864 TATCAAAGCTTACCAG
1 TATCAAAGCTTACCAG
*
5862880 TATCAAAGCTTAGCAG
1 TATCAAAGCTTACCAG
5862896 T
1 T
5862897 GGTGATATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (16 bp):
TATCAAAGCTTACCAG
Found at i:5871299 original size:8 final size:8
Alignment explanation
Indices: 5871281--5871310 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5871271 TACGATTTAT
5871281 TATTAAAAA
1 TATT-AAAA
5871290 TATTAAAA
1 TATTAAAA
5871298 TATTAAAA
1 TATTAAAA
5871306 TATTA
1 TATTA
5871311 TTATATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATTAAAA
Found at i:5871718 original size:20 final size:21
Alignment explanation
Indices: 5871690--5871734 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5871680 ATAATTAAAT
* * *
5871690 TTAATTAAA-AATATTTTTTA
1 TTAAATAAATAATAATTTTAA
5871710 TTAAATAAATAATAATTTTAA
1 TTAAATAAATAATAATTTTAA
5871731 TTAA
1 TTAA
5871735 TTTGAATCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAATAAATAATAATTTTAA
Found at i:5873129 original size:4 final size:4
Alignment explanation
Indices: 5873120--5873148 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5873110 ATCAGCCCAT
5873120 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
5873149 GAGTTTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5874489 original size:3 final size:3
Alignment explanation
Indices: 5874476--5874518 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5874466 GAGCAAAATG
*
5874476 ATA AGA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5874519 GAGATTGGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5876212 original size:19 final size:19
Alignment explanation
Indices: 5876175--5876213 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5876165 AAAAATTCAT
* *
5876175 ATATTTTAATATTTTAAAA
1 ATATTTTAATACTTAAAAA
*
5876194 ATATTTTATTACTTAAAAA
1 ATATTTTAATACTTAAAAA
5876213 A
1 A
5876214 ATAAGTTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTTAATACTTAAAAA
Found at i:5877753 original size:22 final size:24
Alignment explanation
Indices: 5877720--5877763 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5877710 TTTTTTATTT
5877720 TTTTCATATTTT-ATCATATTTAA
1 TTTTCATATTTTAATCATATTTAA
*
5877743 TTTT-ATATTTTAATTATATTT
1 TTTTCATATTTTAATCATATTT
5877764 TATAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTCATATTTTAATCATATTTAA
Found at i:5877777 original size:16 final size:16
Alignment explanation
Indices: 5877725--5877785 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
5877715 TATTTTTTTC
*
5877725 ATATTTTATCATATTT
1 ATATTTTATAATATTT
* *
5877741 A-ATTTTATATTTTAATT
1 ATATTTTATA--ATATTT
5877758 ATATTTTATAATATTT
1 ATATTTTATAATATTT
*
5877774 ATATTATATAAT
1 ATATTTTATAAT
5877786 TATATCATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 7 0.19
16 16 0.44
17 5 0.14
18 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTTATAATATTT
Found at i:5878862 original size:9 final size:9
Alignment explanation
Indices: 5878849--5878889 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
5878839 TTAATTTATT
*
5878849 AATAATAAT
1 AATAATAAG
5878858 AATAATAAG
1 AATAATAAG
5878867 AATAATAAG
1 AATAATAAG
*
5878876 AAGAATAAG
1 AATAATAAG
5878885 AATAA
1 AATAA
5878890 AGATAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (9 bp):
AATAATAAG
Found at i:5878945 original size:27 final size:27
Alignment explanation
Indices: 5878885--5878951 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 27
5878875 GAAGAATAAG
*
5878885 AATAAAGA-TAAA-TAAAATAAATTTA
1 AATAAAAATTAAATTAAAATAAATTTA
** * *
5878910 TTTATAAATTAAATTAAATTAAATTTA
1 AATAAAAATTAAATTAAAATAAATTTA
*
5878937 AATAAAAATAAAATT
1 AATAAAAATTAAATT
5878952 TACTTATTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 23 0.74
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (27 bp):
AATAAAAATTAAATTAAAATAAATTTA
Found at i:5884022 original size:2 final size:2
Alignment explanation
Indices: 5884017--5884057 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
5884007 ATTATACTCT
* *
5884017 TA TA TA TA TA TA TA TA TA AA TA TA TA -A TA TA AA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5884057 T
1 T
5884058 TAATGTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5884067 original size:19 final size:19
Alignment explanation
Indices: 5884044--5884104 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
5884034 AAATATATAA
5884044 TATAAATATAATATTAATG
1 TATAAATATAATATTAATG
** * *
5884063 TATAAATATTTTA-AAATT
1 TATAAATATAATATTAATG
5884081 TATATAATATAAT-TTAATG
1 TATA-AATATAATATTAATG
5884100 TATAA
1 TATAA
5884105 TAATTTATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
18 8 0.25
19 24 0.75
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TATAAATATAATATTAATG
Found at i:5884952 original size:6 final size:6
Alignment explanation
Indices: 5884943--5884979 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
5884933 CTTATTCTTC
*
5884943 TTCTGG TTCTGG TTCTGG TTCTGG TTCTAG TTCTGG T
1 TTCTGG TTCTGG TTCTGG TTCTGG TTCTGG TTCTGG T
5884980 CTATGGATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.16, G:0.30, T:0.51
Consensus pattern (6 bp):
TTCTGG
Found at i:5884958 original size:18 final size:18
Alignment explanation
Indices: 5884937--5884977 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5884927 CTTATTCTTA
* *
5884937 TTCTTCTTCTGGTTCTGG
1 TTCTGCTTCTGGTTCTAG
*
5884955 TTCTGGTTCTGGTTCTAG
1 TTCTGCTTCTGGTTCTAG
5884973 TTCTG
1 TTCTG
5884978 GTCTATGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.20, G:0.24, T:0.54
Consensus pattern (18 bp):
TTCTGCTTCTGGTTCTAG
Found at i:5887432 original size:18 final size:18
Alignment explanation
Indices: 5887409--5887461 Score: 81
Period size: 17 Copynumber: 3.0 Consensus size: 18
5887399 TAATCATAGA
5887409 TTTTAAAAATTATAAATT
1 TTTTAAAAATTATAAATT
* *
5887427 TTTTAAAAATCACAAA-T
1 TTTTAAAAATTATAAATT
5887444 TTTTAAAAATTATAAATT
1 TTTTAAAAATTATAAATT
5887462 CTTATAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAAAATTATAAATT
Found at i:5887453 original size:35 final size:33
Alignment explanation
Indices: 5887409--5887482 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
5887399 TAATCATAGA
*
5887409 TTTTAAAAATTATAAATTTTTTAAAAATCACAAAT
1 TTTTAAAAATTATAAA-TTCTT-AAAATCACAAAT
* *
5887444 TTTTAAAAATTATAAATTCTTATAATCACATAT
1 TTTTAAAAATTATAAATTCTTAAAATCACAAAT
5887477 TTTTAA
1 TTTTAA
5887483 TCTCAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 16 0.44
34 4 0.11
35 16 0.44
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (33 bp):
TTTTAAAAATTATAAATTCTTAAAATCACAAAT
Found at i:5887612 original size:22 final size:21
Alignment explanation
Indices: 5887572--5887613 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5887562 ATAAACAATC
5887572 AAAATTATTTTCTTTTAATTA
1 AAAATTATTTTCTTTTAATTA
5887593 AAAATT-TTTTCTCTTCTAATT
1 AAAATTATTTTCT-TT-TAATT
5887614 CTGTATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
AAAATTATTTTCTTTTAATTA
Found at i:5887976 original size:19 final size:18
Alignment explanation
Indices: 5887926--5887977 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
5887916 GATTTAATTA
*
5887926 ATTTTTAATATTATGTGTT
1 ATTTTTAAT-TTATGTATT
* *
5887945 ATATATAATTTTATGTATT
1 ATTTTTAA-TTTATGTATT
5887964 AGTTTTTAATTTAT
1 A-TTTTTAATTTAT
5887978 TAAATAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (18 bp):
ATTTTTAATTTATGTATT
Found at i:5888274 original size:15 final size:14
Alignment explanation
Indices: 5888246--5888283 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
5888236 AAACTTTATT
5888246 AAAA-ATAAAATAA
1 AAAATATAAAATAA
5888259 AAAATATAATAATAA
1 AAAATATAA-AATAA
5888274 AAAAT-TAAAA
1 AAAATATAAAA
5888284 AATCGAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
15 10 0.43
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATATAAAATAA
Found at i:5890644 original size:28 final size:29
Alignment explanation
Indices: 5890613--5890669 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
5890603 TGAAAAAGAG
*
5890613 AAAATATAAAA-AA-TAAAAATTTTCAAAA
1 AAAATATAAAAGAACAAAAAATTTT-AAAA
*
5890641 AAAATTTAAAAGAACAAAAAATTTTAAAA
1 AAAATATAAAAGAACAAAAAATTTTAAAA
5890670 CCCCACAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
29 6 0.24
30 9 0.36
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (29 bp):
AAAATATAAAAGAACAAAAAATTTTAAAA
Found at i:5890927 original size:21 final size:21
Alignment explanation
Indices: 5890902--5890941 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5890892 GATCTATAAG
5890902 AATTTCTAAAA-TTTAAAAATA
1 AATTTC-AAAATTTTAAAAATA
5890923 AATTTCAAAATTTTAAAAA
1 AATTTCAAAATTTTAAAAA
5890942 ATTGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTCAAAATTTTAAAAATA
Found at i:5891945 original size:14 final size:15
Alignment explanation
Indices: 5891913--5891982 Score: 67
Period size: 14 Copynumber: 4.7 Consensus size: 15
5891903 ATATTATATT
*
5891913 TAATA-AATATAAAA
1 TAATATAATATAATA
5891927 TTAATATAATA-AATA
1 -TAATATAATATAATA
5891942 TAAT-TAAATATAAT-
1 TAATAT-AATATAATA
5891956 TAATATAATATAATA
1 TAATATAATATAATA
*
5891971 TATATATGATAT
1 TA-ATATAATAT
5891983 TTTTATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
13 1 0.02
14 20 0.43
15 14 0.30
16 12 0.26
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (15 bp):
TAATATAATATAATA
Found at i:5891953 original size:19 final size:19
Alignment explanation
Indices: 5891913--5891974 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 19
5891903 ATATTATATT
5891913 TAATAAATATAAAATT-AATA
1 TAATAAATAT--AATTAAATA
5891933 TAATAAATATAATTAAATA
1 TAATAAATATAATTAAATA
*
5891952 TAATTAATATAATATAATATA
1 TAATAAATATAAT-TAA-ATA
5891973 TA
1 TA
5891975 TATGATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
18 4 0.11
19 16 0.42
20 13 0.34
21 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAAATATAATTAAATA
Found at i:5892524 original size:18 final size:18
Alignment explanation
Indices: 5892484--5892523 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5892474 TATTGGTGAT
*
5892484 TTTTATTATATTTATATA
1 TTTTATTATATTTAAATA
5892502 TTTTATTATATTTAAAATA
1 TTTTATTATATTT-AAATA
5892521 TTT
1 TTT
5892524 AAATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTATATTTAAATA
Found at i:5892534 original size:40 final size:44
Alignment explanation
Indices: 5892489--5892569 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
5892479 GTGATTTTTA
*
5892489 TTATATTTATAT-ATTTT-AT-TATA-TTTAAAATATTTAAATT
1 TTATATTTATATAATTTTAATATAAATTTTAAAATATTTAAATT
5892529 TTATATTTATATAAATTTTAATATAAATTTTAAAATATTTA
1 TTATATTTATAT-AATTTTAATATAAATTTTAAAATATTTA
5892570 TTTATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
40 12 0.34
42 5 0.14
43 2 0.06
44 3 0.09
45 13 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (44 bp):
TTATATTTATATAATTTTAATATAAATTTTAAAATATTTAAATT
Found at i:5892566 original size:14 final size:12
Alignment explanation
Indices: 5892537--5892561 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5892527 TTTTATATTT
5892537 ATATAAATTTTA
1 ATATAAATTTTA
5892549 ATATAAATTTTA
1 ATATAAATTTTA
5892561 A
1 A
5892562 AATATTTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATAAATTTTA
Found at i:5892625 original size:29 final size:27
Alignment explanation
Indices: 5892555--5892628 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 27
5892545 TTTAATATAA
5892555 ATTTTAAAATATTTATTTATTTATTTT
1 ATTTTAAAATATTTATTTATTTATTTT
*
5892582 ATATTAATAATATTT-TTATATTATATTTT
1 ATTTTAA-AATATTTATT-TATT-TATTTT
*
5892611 ATTTTTAAAAAATTTATT
1 A-TTTTAAAATATTTATT
5892629 AGTTTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 8 0.21
28 11 0.28
29 13 0.33
30 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTTAAAATATTTATTTATTTATTTT
Found at i:5892644 original size:17 final size:18
Alignment explanation
Indices: 5892613--5892646 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5892603 TATATTTTAT
5892613 TTTTAAAAAATTTATTAG
1 TTTTAAAAAATTTATTAG
5892631 TTTTAAAAAA-TTATTA
1 TTTTAAAAAATTTATTA
5892647 TTACTTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTAAAAAATTTATTAG
Found at i:5893000 original size:24 final size:24
Alignment explanation
Indices: 5892964--5893014 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
5892954 TAGATATAGA
5892964 TTAAAAAATTATTTAAT-TATTAAT
1 TTAAAAAATTATTTAATAT-TTAAT
*
5892988 TTAAAATAA-TATTTTATATTTAAT
1 TTAAAA-AATTATTTAATATTTAAT
5893012 TTA
1 TTA
5893015 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAAAAAATTATTTAATATTTAAT
Found at i:5893243 original size:23 final size:23
Alignment explanation
Indices: 5893191--5893244 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
5893181 ATTTAAGAGT
*
5893191 AAATAAAAATAAAAATCATATTT
1 AAATAAAAATAAAAATCATATTA
*
5893214 AATTAAAAATTAATAAAT-A-ATTA
1 AAATAAAAA-TAA-AAATCATATTA
5893237 AAATAAAA
1 AAATAAAA
5893245 TACTAATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 18 0.69
24 4 0.15
25 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATAAAAATAAAAATCATATTA
Found at i:5894540 original size:15 final size:16
Alignment explanation
Indices: 5894520--5894552 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5894510 TTCAAAACAC
*
5894520 TTTCAAA-CACATTTT
1 TTTCAAATCAAATTTT
5894535 TTTCAAATCAAATTTT
1 TTTCAAATCAAATTTT
5894551 TT
1 TT
5894553 ATAATCACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTCAAATCAAATTTT
Found at i:5895719 original size:6 final size:6
Alignment explanation
Indices: 5895708--5895735 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5895698 TATTTCTTAA
5895708 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
5895736 TTATCGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:5896344 original size:23 final size:24
Alignment explanation
Indices: 5896306--5896358 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
5896296 AAATCTTCAG
* *
5896306 AAATAAAAATTCAAAATTCCAGAA
1 AAATAAAAAATCAAAATTCCAAAA
*
5896330 AAATAAAAAAT-AAAATTTCAAAA
1 AAATAAAAAATCAAAATTCCAAAA
5896353 AAATAA
1 AAATAA
5896359 GGAAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATAAAAAATCAAAATTCCAAAA
Found at i:5896508 original size:5 final size:5
Alignment explanation
Indices: 5896494--5896522 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5896484 AGAAATTCAG
5896494 AAAT- AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
5896523 TGAGGGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:5901319 original size:32 final size:32
Alignment explanation
Indices: 5901283--5901366 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
5901273 TAATTATTCG
*
5901283 TAAATTTAATAAATATTAAATAAAATTACTTA
1 TAAATTTAATAAATATTAAACAAAATTACTTA
* * *
5901315 TAAATTTGATAAATATTAGACATAATTACTTA
1 TAAATTTAATAAATATTAAACAAAATTACTTA
5901347 TAAATTTAAT-AATCATTAAA
1 TAAATTTAATAAAT-ATTAAA
5901367 AAATTTCAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 3 0.07
32 42 0.93
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (32 bp):
TAAATTTAATAAATATTAAACAAAATTACTTA
Found at i:5901531 original size:17 final size:17
Alignment explanation
Indices: 5901468--5901531 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
5901458 TTGACGAGTA
5901468 TTTTATATATAAA-ATT
1 TTTTATATATAAATATT
* * *
5901484 TATTTAT-TCTTATTATT
1 T-TTTATATATAAATATT
* *
5901501 TTTTATTTAAAAATATT
1 TTTTATATATAAATATT
5901518 TTTTATATATAAAT
1 TTTTATATATAAAT
5901532 TAAAATATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
16 9 0.25
17 27 0.75
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATATATAAATATT
Found at i:5901592 original size:15 final size:14
Alignment explanation
Indices: 5901550--5901598 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
5901540 ATACAATCCG
5901550 ATAAATCTAAAACA-
1 ATAAATC-AAAACAT
*
5901564 ATACATCAAAACAT
1 ATAAATCAAAACAT
*
5901578 ATCAAATCAATACAT
1 AT-AAATCAAAACAT
5901593 ATAAAT
1 ATAAAT
5901599 ATCAGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.20
14 12 0.40
15 12 0.40
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAATCAAAACAT
Found at i:5901828 original size:4 final size:4
Alignment explanation
Indices: 5901819--5901843 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5901809 TAGGCTTTAG
5901819 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
5901844 TTTTGCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:5906512 original size:27 final size:27
Alignment explanation
Indices: 5906468--5906522 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5906458 TATGATTATG
* *
5906468 ATATGAATAGTACGAATTACACAAATA
1 ATATGAATAATACAAATTACACAAATA
* *
5906495 ATATGAATAATACAAATTGCACGAATA
1 ATATGAATAATACAAATTACACAAATA
5906522 A
1 A
5906523 ACAATTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (27 bp):
ATATGAATAATACAAATTACACAAATA
Found at i:5906648 original size:32 final size:32
Alignment explanation
Indices: 5906605--5906709 Score: 128
Period size: 32 Copynumber: 3.4 Consensus size: 32
5906595 CTTACGTGTT
* *
5906605 AAAATTTATATAATATAAATTATTAAGATATC
1 AAAATTTATATAACACAAATTATTAAGATATC
* *
5906637 ACAATTTATATAACACAAATTATTAAGGTATC
1 AAAATTTATATAACACAAATTATTAAGATATC
**
5906669 AAAATTTATAT---AC-AATTATTAACTTATC
1 AAAATTTATATAACACAAATTATTAAGATATC
5906697 AAAATTTATATAA
1 AAAATTTATATAA
5906710 ATATATAATA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
28 24 0.38
29 2 0.03
32 38 0.59
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (32 bp):
AAAATTTATATAACACAAATTATTAAGATATC
Found at i:5906696 original size:28 final size:28
Alignment explanation
Indices: 5906617--5906708 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 28
5906607 AATTTATATA
*
5906617 ATATA-AATTATTAAGATATCACAATTT
1 ATATACAATTATTAAGATATCAAAATTT
*
5906644 ATATAACACAAATTATTAAGGTATCAAAATTT
1 ATAT---AC-AATTATTAAGATATCAAAATTT
**
5906676 ATATACAATTATTAACTTATCAAAATTT
1 ATATACAATTATTAAGATATCAAAATTT
5906704 ATATA
1 ATATA
5906709 AATATATAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.07
28 25 0.45
29 2 0.04
30 1 0.02
32 24 0.43
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (28 bp):
ATATACAATTATTAAGATATCAAAATTT
Found at i:5909373 original size:30 final size:33
Alignment explanation
Indices: 5909311--5909381 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 33
5909301 TTTGTTAGTA
*
5909311 ATTTATATTATATAAATTTTAATATATTTAAAT
1 ATTTATATTATATAAATTTTAATATATATAAAT
*
5909344 ATTTATATTA-AT-AA-TTTAATTTATATAAAT
1 ATTTATATTATATAAATTTTAATATATATAAAT
*
5909374 TTTTATAT
1 ATTTATAT
5909382 AAATTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 21 0.60
31 2 0.06
32 2 0.06
33 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
ATTTATATTATATAAATTTTAATATATATAAAT
Found at i:5910316 original size:20 final size:20
Alignment explanation
Indices: 5910279--5910317 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5910269 AAAATGTCTT
** *
5910279 TAAATTTTTTTATTTTTAAA
1 TAAATTTTAATATATTTAAA
5910299 TAAATTTTAATATATTTAA
1 TAAATTTTAATATATTTAA
5910318 TATATATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAAATTTTAATATATTTAAA
Found at i:5912063 original size:16 final size:16
Alignment explanation
Indices: 5912017--5912055 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5912007 TTTAATAGAT
* *
5912017 ATTTGAACTCAAATGTA
1 ATTT-AACTAAAATTTA
5912034 ATTTAACTAAAATTTA
1 ATTTAACTAAAATTTA
5912050 ATTTAA
1 ATTTAA
5912056 TAATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTTAACTAAAATTTA
Found at i:5914939 original size:21 final size:22
Alignment explanation
Indices: 5914915--5914964 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
5914905 TCGAAATTAC
* *
5914915 TAAATTAATATTTAA-AATATT
1 TAAATTAATATTTAATAAAATA
*
5914936 TAAAAT-ATATTTAATAAAATA
1 TAAATTAATATTTAATAAAATA
5914957 TAAATTAA
1 TAAATTAA
5914965 ATCCATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.35
21 14 0.61
22 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTAATATTTAATAAAATA
Found at i:5915002 original size:23 final size:22
Alignment explanation
Indices: 5914957--5915033 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
5914947 TAATAAAATA
* *
5914957 TAAATTAAATC-CATTTAAACT
1 TAAATTAAAGCTCATCTAAACT
5914978 TAAATTAAAAGCTCATCTAAACT
1 TAAATT-AAAGCTCATCTAAACT
* *
5915001 TAAATTTAAGTTCATCTAAA-T
1 TAAATTAAAGCTCATCTAAACT
5915022 CTAAATTTAAAG
1 -TAAA-TTAAAG
5915034 TCTAATTAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
21 7 0.15
22 20 0.43
23 20 0.43
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAATTAAAGCTCATCTAAACT
Found at i:5918131 original size:21 final size:21
Alignment explanation
Indices: 5918090--5918133 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5918080 TATATATTTA
* **
5918090 ATTTTTAAAAATTTATTAATT
1 ATTTTAAAAAATTTAAAAATT
5918111 ATTTTAAAAAATTTAAAAATT
1 ATTTTAAAAAATTTAAAAATT
5918132 AT
1 AT
5918134 ATTTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTAAAAAATTTAAAAATT
Found at i:5918174 original size:25 final size:26
Alignment explanation
Indices: 5918121--5918174 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
5918111 ATTTTAAAAA
* ***
5918121 ATTTAAAAATTATATTTTATATTTTT
1 ATTTAAAAATTATATTATATATAAAT
5918147 ATTTAAAAA-TATATTATATATAAAT
1 ATTTAAAAATTATATTATATATAAAT
5918172 ATT
1 ATT
5918175 AAATATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTAAAAATTATATTATATATAAAT
Found at i:5918175 original size:13 final size:13
Alignment explanation
Indices: 5918157--5918187 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5918147 ATTTAAAAAT
*
5918157 ATATTATATATAA
1 ATATTAAATATAA
5918170 ATATTAAATATAA
1 ATATTAAATATAA
5918183 ATATT
1 ATATT
5918188 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTAAATATAA
Found at i:5918680 original size:2 final size:2
Alignment explanation
Indices: 5918675--5918703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5918665 TGAAAAAAAC
5918675 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
5918704 ATAGAACAAT
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:5921397 original size:13 final size:13
Alignment explanation
Indices: 5921381--5921405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5921371 ACAAGAAAGG
5921381 GATGCTTGAGAGA
1 GATGCTTGAGAGA
5921394 GATGCTTGAGAG
1 GATGCTTGAGAG
5921406 GGATACAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.40, T:0.24
Consensus pattern (13 bp):
GATGCTTGAGAGA
Found at i:5921513 original size:27 final size:27
Alignment explanation
Indices: 5921475--5921573 Score: 148
Period size: 27 Copynumber: 3.7 Consensus size: 27
5921465 ACATGTCACT
* *
5921475 ATTTTTGACAAATA-AAAAGAAACCACC
1 ATTTTTGACAAACACAAAA-TAACCACC
5921502 ATTTTTGACAAACACAAAATAACCACC
1 ATTTTTGACAAACACAAAATAACCACC
*
5921529 ATTTTTGACAAATACAAAATAACCACC
1 ATTTTTGACAAACACAAAATAACCACC
5921556 ATTTTTGACAAACA-AAAA
1 ATTTTTGACAAACACAAAA
5921574 GTGGCTTTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
26 4 0.06
27 59 0.88
28 4 0.06
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAACACAAAATAACCACC
Found at i:5926484 original size:35 final size:35
Alignment explanation
Indices: 5926438--5926510 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
5926428 TCTAATCTGC
5926438 TCAATAGATTTAATTTATTCGACTTGAGTTTTTAG
1 TCAATAGATTTAATTTATTCGACTTGAGTTTTTAG
5926473 TCAATAGATTTAATTTATTCGACTTGAGTTTTTAG
1 TCAATAGATTTAATTTATTCGACTTGAGTTTTTAG
5926508 TCA
1 TCA
5926511 TAATTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (35 bp):
TCAATAGATTTAATTTATTCGACTTGAGTTTTTAG
Found at i:5927096 original size:108 final size:108
Alignment explanation
Indices: 5926811--5927518 Score: 579
Period size: 108 Copynumber: 6.4 Consensus size: 108
5926801 GACACGGAAT
* * * * * *
5926811 ATTTCAACTCCATCAGTATGCGATTCTGTTTCGACTGCTTCTATTGTTGATCTGGACGCGATAGT
1 ATTTCAACTCCATCAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTGATCTGGATGCTATGGT
* * * *
5926876 GGATGAACTTATAATTCCCCCAGACGCTGAATTTATCC-CTGAG
66 GGATGAACTTACAACTCCCCTAGACGCAGAATTTATCCTC-GAG
* * * * *
5926919 ATTTCAGCTCCATCCCTAACAACATGAAATTCTGTTTCGACTGCTTTTGTTGTTGATTTGGATGC
1 ATTTCAACTCCA----T--CAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTGATCTGGATGC
* *
5926984 TATGGTAGATGAACTTACAACTCCCCTAGATGCAGAATTTATCCTCGAG
60 TATGGTGGATGAACTTACAACTCCCCTAGACGCAGAATTTATCCTCGAG
** * * * *
5927033 ATTTCAACTCTGTCAGCCTGAGATTCTATTTTGACTGCTTCTGTTGTTGAACTGGATGCTATGGT
1 ATTTCAACTCCATCAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTGATCTGGATGCTATGGT
* * *
5927098 GGATGAACTTACAGCTACCCC-AGATG-TGAAATTTAT-CTCAGAG
66 GGATGAACTTACAACT-CCCCTAGACGCAG-AATTTATCCTC-GAG
* * * *
5927141 ATTTCATCTCCATCAGTATGAGATTCTGTTTCG-CTTGCTTCTGTTGTTGATGTGGATGGTATGG
1 ATTTCAACTCCATCAGCATGAGATTCTGTTTCGAC-TGCTTCTGTTGTTGATCTGGATGCTATGG
** *** * * *
5927205 TGGATGATTTTACAACT-CCCTCAGACATGGAATTTGTCCCCAAG
65 TGGATGAACTTACAACTCCCCT-AGACGCAGAATTTATCCTCGAG
* * **
5927249 ATTTCAACTTCGTCCCTAACAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGC
1 ATTTCAA---C-T-CC-ATCAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTGATCTGGATGC
* * * * * ** *
5927314 TATAGTAGATGAACGTACTACTCCTCTAGACATAGAATTTGT-CTCTGAG
60 TATGGTGGATGAACTTACAACTCCCCTAGACGCAGAATTTATCCTC-GAG
* * * * * * *
5927363 ATTTCAACTCCATCACCATTAGATTCTATATCGACTGCTTCTATTGTTGATCTGGATGCCATAGT
1 ATTTCAACTCCATCAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTGATCTGGATGCTATGGT
* *
5927428 GGATGAACTTAAAACT-CCCTCAGACGC-GAAATTTATCCTCGGG
66 GGATGAACTTACAACTCCCCT-AGACGCAG-AATTTATCCTCGAG
5927471 ATTTCAACTCCATCGATAATAGCATGAGATTCTGTTTCGACTGCTTCT
1 ATTTCAACTCCATC------AGCATGAGATTCTGTTTCGACTGCTTCT
5927519 ATTTTGCAAT
Statistics
Matches: 476, Mismatches: 91, Indels: 60
0.76 0.15 0.10
Matches are distributed among these distances:
106 3 0.01
107 9 0.02
108 249 0.52
109 12 0.03
110 2 0.00
111 2 0.00
112 2 0.00
113 4 0.01
114 188 0.39
115 5 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (108 bp):
ATTTCAACTCCATCAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTGATCTGGATGCTATGGT
GGATGAACTTACAACTCCCCTAGACGCAGAATTTATCCTCGAG
Found at i:5927279 original size:222 final size:220
Alignment explanation
Indices: 5926832--5927518 Score: 592
Period size: 222 Copynumber: 3.1 Consensus size: 220
5926822 ATCAGTATGC
* * ** * * * * * *
5926832 GATTCTGTTTCGACTGCTTCTATTGTTGATCTGGACGCGATAGTGGATGAACTTA-TAATTCCCC
1 GATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACT-ACTCCTC
* * * * *
5926896 CAGACGCT-GAATTTATCCCTGAGATTTCAGCTCCATCCCTAACAACATGAAATTCTGTTTCGAC
65 CAGAC-ATAGAATTTATCTCAGAGATTTCAACTCCAT--C--AC--CATGAGATTCTGTTTCGAC
* * *
5926960 TGCTTTTGTTGTTGATTTGGATGCTATGGTAGATGAACTTACAACTCCC-CTAG--ATGCAGAAT
123 TGCTTCTGTTGTTGATCTGGATGCTATGGTGGATGAACTTACAACTCCCTC-AGACATG--GAAT
* *
5927022 TTATCCTCGAGATTTCAAC-TCT-GT--CAGCCTGA
185 TTATCCTCGAGATTTCAACTTCTCATAACAGCATGA
* * ** * * *
5927054 GATTCTATTTTGACTGCTTCTGTTGTTGAA-CTGGATGCTATGGTGGATGAACTTAC-AGCTACC
1 GATTCTGTTTCGACTGCTTCTGTTGTT-AATCCAGATGCTATAGTAGATGAACGTACTA-CT-CC
** * **
5927117 -CCAGATGT-GAAATTTATCTCAGAGATTTCATCTCCATCAGTATGAGATTCTGTTTCG-CTTGC
63 TCCAGACATAG-AATTTATCTCAGAGATTTCAACTCCATCACCATGAGATTCTGTTTCGAC-TGC
* * ** *
5927179 TTCTGTTGTTGATGTGGATGGTATGGTGGATGATTTTACAACTCCCTCAGACATGGAATTTGTCC
126 TTCTGTTGTTGATCTGGATGCTATGGTGGATGAACTTACAACTCCCTCAGACATGGAATTTATCC
* * *
5927244 CCAAGATTTCAACTTCGTCCCTAACAGCATGA
191 TCGAGATTTCAACTTC-T-CATAACAGCATGA
*
5927276 GATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACTACTCCTCT
1 GATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACTACTCCTCC
* * * * * *
5927341 AGACATAGAATTTGTCTCTGAGATTTCAACTCCATCACCATTAGATTCTATATCGACTGCTTCTA
66 AGACATAGAATTTATCTCAGAGATTTCAACTCCATCACCATGAGATTCTGTTTCGACTGCTTCTG
* * * ** * *
5927406 TTGTTGATCTGGATGCCATAGTGGATGAACTTAAAACTCCCTCAGACGCGAAATTTATCCTCGGG
131 TTGTTGATCTGGATGCTATGGTGGATGAACTTACAACTCCCTCAGACATGGAATTTATCCTCGAG
* *
5927471 ATTTCAACTCCATCGATAATAGCATGA
196 ATTTCAACTTC-TC-ATAACAGCATGA
5927498 GATTCTGTTTCGACTGCTTCT
1 GATTCTGTTTCGACTGCTTCT
5927519 ATTTTGCAAT
Statistics
Matches: 380, Mismatches: 64, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
215 1 0.00
216 80 0.21
217 3 0.01
218 5 0.01
220 2 0.01
221 8 0.02
222 275 0.72
223 6 0.02
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (220 bp):
GATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACTACTCCTCC
AGACATAGAATTTATCTCAGAGATTTCAACTCCATCACCATGAGATTCTGTTTCGACTGCTTCTG
TTGTTGATCTGGATGCTATGGTGGATGAACTTACAACTCCCTCAGACATGGAATTTATCCTCGAG
ATTTCAACTTCTCATAACAGCATGA
Found at i:5927420 original size:330 final size:330
Alignment explanation
Indices: 5926811--5927521 Score: 824
Period size: 330 Copynumber: 2.1 Consensus size: 330
5926801 GACACGGAAT
*
5926811 ATTTCAACTCCATCAGTATGCGATTCTGTTTCGACTGCTTCTATTGTTGATCTGGACGCGATAGT
1 ATTTCAACTCCATCAGTATGAGATTCTGTTTCGACTGCTTCTATTGTTGATCTGGACGCGATAGT
* * * ** *
5926876 GGATGAACTTATAATTCCCCCAGACGCTGAATTTATCCCTGAGATTTCAGCTCCATCCCTAACAA
66 GGATGAACTTACAACTCCCCCAGACGATGAATTTATCCCCAAGATTTCAACTCCATCCCTAACAA
* * *** * *
5926941 CATGAAATTCTGTTTCGACTGCTTTTGTTGTTGATTTGGATGCTATGGTAGATGAACTTACAACT
131 CATGAAATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACAACT
** ** * *
5927006 CCCCTAGATGCAGAATTTATCCTCGAGATTTCAACTCTGTCAGCCTGAGATTCTATTTTGACTGC
196 CCCCTAGACACAGAATTTATCCTCGAGATTTCAACTCCATCAGCCTGAGATTCTATATCGACTGC
* * * * * * *
5927071 TTCTGTTGTTGAACTGGATGCTATGGTGGATGAACTTACAGCTACCC-CAGATGTGAAATTTAT-
261 TTCTATTGTTGAACTGGATGCCATAGTGGATGAACTTAAAACT-CCCTCAGACGCGAAATTTATC
5927134 CTCAGAG
325 CTC-GAG
* * * * *
5927141 ATTTCATCTCCATCAGTATGAGATTCTGTTTCG-CTTGCTTCTGTTGTTGATGTGGATG-GTATG
1 ATTTCAACTCCATCAGTATGAGATTCTGTTTCGAC-TGCTTCTATTGTTGATCTGGACGCG-ATA
** * * * *
5927204 GTGGATGATTTTACAACTCCCTCAGAC-ATGGAATTTGTCCCCAAGATTTCAACTTCGTCCCTAA
64 GTGGATGAACTTACAACTCCCCCAGACGAT-GAATTTATCCCCAAGATTTCAACTCCATCCCTAA
* * *
5927268 CAGCATGAGATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACT
128 CAACATGAAATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACA
* * * *
5927333 ACTCCTCTAGACATAGAATTTGT-CTCTGAGATTTCAACTCCATCA-CCATTAGATTCTATATCG
193 ACTCCCCTAGACACAGAATTTATCCTC-GAGATTTCAACTCCATCAGCC-TGAGATTCTATATCG
*
5927396 ACTGCTTCTATTGTTGATCTGGATGCCATAGTGGATGAACTTAAAACTCCCTCAGACGCGAAATT
256 ACTGCTTCTATTGTTGAACTGGATGCCATAGTGGATGAACTTAAAACTCCCTCAGACGCGAAATT
*
5927461 TATCCTCGGG
321 TATCCTCGAG
*
5927471 ATTTCAACTCCATCGATAATAGCATGAGATTCTGTTTCGACTGCTTCTATT
1 ATTTCAACTCCATC------AGTATGAGATTCTGTTTCGACTGCTTCTATT
5927522 TTGCAATCAT
Statistics
Matches: 317, Mismatches: 50, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
329 11 0.03
330 275 0.87
331 3 0.01
336 27 0.09
337 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (330 bp):
ATTTCAACTCCATCAGTATGAGATTCTGTTTCGACTGCTTCTATTGTTGATCTGGACGCGATAGT
GGATGAACTTACAACTCCCCCAGACGATGAATTTATCCCCAAGATTTCAACTCCATCCCTAACAA
CATGAAATTCTGTTTCGACTGCTTCTGTTGTTAATCCAGATGCTATAGTAGATGAACGTACAACT
CCCCTAGACACAGAATTTATCCTCGAGATTTCAACTCCATCAGCCTGAGATTCTATATCGACTGC
TTCTATTGTTGAACTGGATGCCATAGTGGATGAACTTAAAACTCCCTCAGACGCGAAATTTATCC
TCGAG
Found at i:5929238 original size:2 final size:2
Alignment explanation
Indices: 5929233--5929263 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5929223 TCACATAACC
5929233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5929264 TTGTTTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5929412 original size:21 final size:23
Alignment explanation
Indices: 5929386--5929429 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
5929376 GTATTTATTT
*
5929386 TTTTAATTA-AATGT-TATTTAA
1 TTTTAATTATAATATATATTTAA
5929407 TTTTAATTATAATATATATTTAA
1 TTTTAATTATAATATATATTTAA
5929430 AATATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATTATAATATATATTTAA
Found at i:5931823 original size:198 final size:198
Alignment explanation
Indices: 5931485--5931880 Score: 792
Period size: 198 Copynumber: 2.0 Consensus size: 198
5931475 CTAATCATAA
5931485 ATATTATAATAAGACTTATTACACCTAATCAACATACAATATTGGTCTTGGTCGTTGTTTACGAT
1 ATATTATAATAAGACTTATTACACCTAATCAACATACAATATTGGTCTTGGTCGTTGTTTACGAT
5931550 ATGAAGTAAGCCATCTTAACACTCTTTTATTTTGGAGTAACTAAATATTTTTCTAAATTAGGTGC
66 ATGAAGTAAGCCATCTTAACACTCTTTTATTTTGGAGTAACTAAATATTTTTCTAAATTAGGTGC
5931615 ACCATTTTATATAAAGTTTAAGTGAGAAAAGCAACACTTGGTTTTTTTCCTCAATAAATTAGAAG
131 ACCATTTTATATAAAGTTTAAGTGAGAAAAGCAACACTTGGTTTTTTTCCTCAATAAATTAGAAG
5931680 TTT
196 TTT
5931683 ATATTATAATAAGACTTATTACACCTAATCAACATACAATATTGGTCTTGGTCGTTGTTTACGAT
1 ATATTATAATAAGACTTATTACACCTAATCAACATACAATATTGGTCTTGGTCGTTGTTTACGAT
5931748 ATGAAGTAAGCCATCTTAACACTCTTTTATTTTGGAGTAACTAAATATTTTTCTAAATTAGGTGC
66 ATGAAGTAAGCCATCTTAACACTCTTTTATTTTGGAGTAACTAAATATTTTTCTAAATTAGGTGC
5931813 ACCATTTTATATAAAGTTTAAGTGAGAAAAGCAACACTTGGTTTTTTTCCTCAATAAATTAGAAG
131 ACCATTTTATATAAAGTTTAAGTGAGAAAAGCAACACTTGGTTTTTTTCCTCAATAAATTAGAAG
5931878 TTT
196 TTT
5931881 TCGGGTAGCA
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (198 bp):
ATATTATAATAAGACTTATTACACCTAATCAACATACAATATTGGTCTTGGTCGTTGTTTACGAT
ATGAAGTAAGCCATCTTAACACTCTTTTATTTTGGAGTAACTAAATATTTTTCTAAATTAGGTGC
ACCATTTTATATAAAGTTTAAGTGAGAAAAGCAACACTTGGTTTTTTTCCTCAATAAATTAGAAG
TTT
Found at i:5932896 original size:3 final size:3
Alignment explanation
Indices: 5932888--5932934 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
5932878 GTTCCTTCAA
5932888 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5932935 CCTTTCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5933475 original size:48 final size:48
Alignment explanation
Indices: 5933416--5933510 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
5933406 GTTGCCCTCT
* *
5933416 AAAAAAATTCTTTAAAGTCTTGTTATAAATTTATTGCAATGTGAAAGA
1 AAAAAAATTCTTCAAAGTCTTATTATAAATTTATTGCAATGTGAAAGA
* *
5933464 AAAAAAATTCTTCAGAGTCTTATTATAATTTTATTGCAATGTGAAAG
1 AAAAAAATTCTTCAAAGTCTTATTATAAATTTATTGCAATGTGAAAG
5933511 TTTAACGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (48 bp):
AAAAAAATTCTTCAAAGTCTTATTATAAATTTATTGCAATGTGAAAGA
Found at i:5934281 original size:17 final size:17
Alignment explanation
Indices: 5934226--5934301 Score: 63
Period size: 16 Copynumber: 4.6 Consensus size: 17
5934216 GATCCGAATC
* *
5934226 CAAAATAACTT-AAATT
1 CAAAATAACTTCGAACT
5934242 CAAAATAA--TCGAAACT
1 CAAAATAACTTCG-AACT
* *
5934258 AAAAATAACTTTGAA-T
1 CAAAATAACTTCGAACT
5934274 CTAAAATAA-TTCGAACT
1 C-AAAATAACTTCGAACT
5934291 CAAAATAACTT
1 CAAAATAACTT
5934302 AAACAATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
14 1 0.02
16 31 0.66
17 13 0.28
18 2 0.04
ACGTcount: A:0.54, C:0.14, G:0.04, T:0.28
Consensus pattern (17 bp):
CAAAATAACTTCGAACT
Found at i:5934296 original size:33 final size:32
Alignment explanation
Indices: 5934204--5934301 Score: 94
Period size: 33 Copynumber: 3.0 Consensus size: 32
5934194 TTAATCAATC
* *
5934204 TGAATTTAAAATGATCCGAA-TCCAAAATAAC-T
1 TGAA-TTAAAATAATTCGAACT-CAAAATAACTT
* *
5934236 TAAATTCAAAATAA-TCGAAACTAAAAATAACTT
1 TGAATT-AAAATAATTCG-AACTCAAAATAACTT
5934269 TGAATCTAAAATAATTCGAACTCAAAATAACTT
1 TGAAT-TAAAATAATTCGAACTCAAAATAACTT
5934302 AAACAATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
31 4 0.07
32 19 0.35
33 27 0.50
34 4 0.07
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (32 bp):
TGAATTAAAATAATTCGAACTCAAAATAACTT
Found at i:5937455 original size:16 final size:16
Alignment explanation
Indices: 5937434--5937486 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5937424 CCTAAACTTG
5937434 AAATAATCCAAATTCA
1 AAATAATCCAAATTCA
** * *
5937450 AAATAATATACACTCA
1 AAATAATCCAAATTCA
5937466 AAATAA-CCAAATTCA
1 AAATAATCCAAATTCA
5937481 AAATAA
1 AAATAA
5937487 CTCAAACCGT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAATCCAAATTCA
Found at i:5937483 original size:15 final size:15
Alignment explanation
Indices: 5937434--5937492 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
5937424 CCTAAACTTG
5937434 AAATAATCCAAATTCA
1 AAATAA-CCAAATTCA
* *
5937450 AAATAA-TATACACTCA
1 AAATAACCA-A-ATTCA
5937466 AAATAACCAAATTCA
1 AAATAACCAAATTCA
5937481 AAATAACTCAAA
1 AAATAAC-CAAA
5937493 CCGTAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.03
15 12 0.34
16 21 0.60
17 1 0.03
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATAACCAAATTCA
Found at i:5942047 original size:20 final size:20
Alignment explanation
Indices: 5942018--5942055 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5942008 TAATAATAAT
*
5942018 TTCTTAAAATATGTTTTTAA
1 TTCTTAAAATAGGTTTTTAA
*
5942038 TTCTTTAAATAGGTTTTT
1 TTCTTAAAATAGGTTTTT
5942056 GAGAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (20 bp):
TTCTTAAAATAGGTTTTTAA
Found at i:5944242 original size:18 final size:18
Alignment explanation
Indices: 5944215--5944260 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5944205 AAAATTTGAA
*
5944215 AAAATCATTTAAGATTTT
1 AAAATGATTTAAGATTTT
5944233 AAAATGATTTAAGATTTT
1 AAAATGATTTAAGATTTT
*
5944251 AAATTGATTT
1 AAAATGATTT
5944261 TTTAACATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (18 bp):
AAAATGATTTAAGATTTT
Found at i:5949563 original size:14 final size:14
Alignment explanation
Indices: 5949544--5949572 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5949534 CATTTAGCCC
5949544 CTTTTTTTTTCCTT
1 CTTTTTTTTTCCTT
5949558 CTTTTTTTTTCCTT
1 CTTTTTTTTTCCTT
5949572 C
1 C
5949573 AATCCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTTTTTTTCCTT
Found at i:5949669 original size:30 final size:30
Alignment explanation
Indices: 5949620--5949680 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
5949610 TACTACTCTT
*
5949620 AAAAATTTAAAGTTCTAT-AATCAAATTAA
1 AAAAATTTAAAGTTCTATAAATAAAATTAA
* *
5949649 AAAAATCTTAAATTTTTATAAATAAAATTAA
1 AAAAAT-TTAAAGTTCTATAAATAAAATTAA
5949680 A
1 A
5949681 TTACACAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.22
30 10 0.37
31 11 0.41
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAAATTTAAAGTTCTATAAATAAAATTAA
Found at i:5949811 original size:71 final size:73
Alignment explanation
Indices: 5949717--5949853 Score: 176
Period size: 71 Copynumber: 1.9 Consensus size: 73
5949707 ATCATACCTG
* *
5949717 ATAAAAAACACAATTAAATTTCTACAAATCA-AAATAAATTAT-ACCCT-A-CAAATTTAAACTT
1 ATAAAAAACACAATTAAACTTCTACAAAT-AGAAATAAATAATAACCCTAATCAAA-TTAAACTT
5949778 ATATAATCAA
64 ATATAATCAA
* *
5949788 ATAAAAAATA-AATTTAAACTTCTACAAATAGAAATAAATAATAACCCTAATCAAATTAATCTTA
1 ATAAAAAACACAA-TTAAACTTCTACAAATAGAAATAAATAATAACCCTAATCAAATTAAACTTA
5949852 TA
65 TA
5949854 AATAAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
70 3 0.05
71 34 0.60
72 5 0.09
73 11 0.19
74 4 0.07
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (73 bp):
ATAAAAAACACAATTAAACTTCTACAAATAGAAATAAATAATAACCCTAATCAAATTAAACTTAT
ATAATCAA
Found at i:5949866 original size:23 final size:21
Alignment explanation
Indices: 5949840--5949889 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
5949830 AACCCTAATC
*
5949840 AAATTAATCTTATAAATAAAAAT
1 AAATTAACCTTA-AAAT-AAAAT
*
5949863 AAATCAAACCTTAAAATAAAAT
1 AAAT-TAACCTTAAAATAAAAT
5949885 AAATT
1 AAATT
5949890 TTAAACTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.39
23 8 0.35
24 6 0.26
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAACCTTAAAATAAAAT
Done.