Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 14 of 349
Found at i:4182137 original size:16 final size:16
Alignment explanation
Indices: 4182051--4182137 Score: 58
Period size: 16 Copynumber: 5.4 Consensus size: 16
4182041 TATTATTTTG
4182051 ATATTTTA-AAATTTAT
1 ATATTTTATAAA-TTAT
4182067 ATATTTTA-AAATT-T
1 ATATTTTATAAATTAT
* *
4182081 ATA-TTTATATATTTT
1 ATATTTTATAAATTAT
*
4182096 AGAATTTTATAAAAAATTAT
1 A-TATTTTAT---AAATTAT
*
4182116 -TTTTTTATAAATTAT
1 ATATTTTATAAATTAT
4182131 ATATTTT
1 ATATTTT
4182138 TTACATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
13 4 0.07
14 8 0.14
15 11 0.20
16 17 0.30
17 5 0.09
18 6 0.11
20 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
ATATTTTATAAATTAT
Found at i:4188768 original size:17 final size:17
Alignment explanation
Indices: 4188742--4188783 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4188732 ATATAAGAAC
*
4188742 ATTTATTATTAAATTAT
1 ATTTAATATTAAATTAT
4188759 ATTTAATATT-AATTAT
1 ATTTAATATTAAATTAT
4188775 -TTTAA-ATTA
1 ATTTAATATTA
4188784 TATAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 5 0.22
16 6 0.26
17 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTAATATTAAATTAT
Found at i:4188822 original size:44 final size:43
Alignment explanation
Indices: 4188759--4188910 Score: 112
Period size: 44 Copynumber: 3.4 Consensus size: 43
4188749 ATTAAATTAT
* *
4188759 ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
1 ATTTATTA-TAATAATTTTAAATTATATAAATTCATATAAGAAA
* * *
4188803 ATTTATTATCATGAATTTTATGAAATTATATATTATT-AT-TAA-ATTAT
1 ATTTATTATAAT-AA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
* * *
4188850 ATTTAATAATAATTATTTTAAATTATACAAATTCATATAAGAAA
1 ATTT-ATTATAATAATTTTAAATTATATAAATTCATATAAGAAA
*
4188894 ATTTATTAGTTATAATT
1 ATTTATTA-TAATAATT
4188911 ATTTTAAATT
Statistics
Matches: 82, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
43 9 0.11
44 30 0.37
45 8 0.10
46 8 0.10
47 18 0.22
48 9 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (43 bp):
ATTTATTATAATAATTTTAAATTATATAAATTCATATAAGAAA
Found at i:4188868 original size:47 final size:46
Alignment explanation
Indices: 4188744--4188876 Score: 111
Period size: 47 Copynumber: 3.0 Consensus size: 46
4188734 ATAAGAACAT
*
4188744 TTATTATTAAATTATATTTAATATTAATTA-TTT-TAAATTATATA
1 TTATTATTAAATTATATTTAATAATAATTATTTTATAAATTATATA
* * * * *
4188788 -AATTCATATAAGA--AAATTT-ATTATCATGAATTTTATGAAATTATATA
1 TTATT-AT-TAA-ATTATATTTAATAATAAT-TATTTTAT-AAATTATATA
4188835 TTATTATTAAATTATATTTAATAATAATTA-TTT-TAAATTATA
1 TTATTATTAAATTATATTTAATAATAATTATTTTATAAATTATA
4188877 CAAATTCATA
Statistics
Matches: 67, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
43 8 0.12
44 16 0.24
45 8 0.12
46 8 0.12
47 18 0.27
48 9 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (46 bp):
TTATTATTAAATTATATTTAATAATAATTATTTTATAAATTATATA
Found at i:4189047 original size:120 final size:120
Alignment explanation
Indices: 4188917--4189442 Score: 807
Period size: 120 Copynumber: 4.4 Consensus size: 120
4188907 AATTATTTTA
* * *
4188917 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACT-TCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTA-TGTCAAATTATATTT
* *
4188981 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATGTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
4189037 AATTTTATTAAA-T-TATA---TAATTAAAATATTTTTAATATTAATTAAT-TCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATT-ATGTCAAATTATATTT
* * *
4189096 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGACTTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
4189152 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTCAAATTATATTTT
* *
4189217 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* * *
4189272 AATTTTACTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTCAAATTATATTTT
4189337 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAG-ATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
4189391 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATGT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGT
4189443 TTAAATATAA
Statistics
Matches: 380, Mismatches: 19, Indels: 15
0.92 0.05 0.04
Matches are distributed among these distances:
115 106 0.28
116 2 0.01
117 4 0.01
118 4 0.01
119 65 0.17
120 199 0.52
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTCAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:4189181 original size:18 final size:17
Alignment explanation
Indices: 4189153--4189187 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4189143 ATTATTAAGA
*
4189153 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
4189170 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
4189188 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:4189307 original size:16 final size:16
Alignment explanation
Indices: 4189286--4189332 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
4189276 TTACTAAATT
4189286 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
4189302 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
4189317 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
4189333 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:4189312 original size:15 final size:15
Alignment explanation
Indices: 4189282--4189332 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
4189272 AATTTTACTA
4189282 AATTAT-ATAT-TTT
1 AATTATAATATATTT
4189295 AATTATAATATATTT
1 AATTATAATATATTT
*
4189310 AATAATAAT-TATGTT
1 AATTATAATATAT-TT
4189325 AAATTATA
1 -AATTATA
4189333 TTTTATAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 6 0.19
14 7 0.22
15 13 0.41
16 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTATAATATATTT
Found at i:4189672 original size:45 final size:44
Alignment explanation
Indices: 4189572--4189681 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 44
4189562 TTTTCCATTA
4189572 TGCTATTACACCTCTATT-C----CATTCAACCAAACATAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACATAAGAT
* * *
4189611 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGT-TGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACA-TAAGA-T
4189656 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
4189682 CCTCTATTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
39 16 0.27
40 1 0.02
44 16 0.27
45 26 0.44
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACATAAGAT
Found at i:4189681 original size:16 final size:16
Alignment explanation
Indices: 4189660--4189713 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
4189650 TTGATTTGCT
4189660 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
4189676 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
4189692 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
4189708 AATACA
1 ATTACA
4189714 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:4206840 original size:12 final size:11
Alignment explanation
Indices: 4206824--4206900 Score: 54
Period size: 12 Copynumber: 7.0 Consensus size: 11
4206814 TATTATTATC
4206824 ATATTATATTA
1 ATATTATATTA
4206835 AGTATTACT-TTA
1 A-TATTA-TATTA
*
4206847 ATATTACATTA
1 ATATTATATTA
4206858 ACTATTATATT-
1 A-TATTATATTA
*
4206869 TTA-T-TATTA
1 ATATTATATTA
*
4206878 CTATTATTATTA
1 ATATTA-TATTA
*
4206890 CTATTATATTA
1 ATATTATATTA
4206901 TTAGTACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 4 0.07
9 3 0.06
10 3 0.06
11 15 0.28
12 28 0.52
13 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (11 bp):
ATATTATATTA
Found at i:4206877 original size:3 final size:3
Alignment explanation
Indices: 4206860--4207013 Score: 55
Period size: 3 Copynumber: 54.3 Consensus size: 3
4206850 TTACATTAAC
* * *
4206860 TAT TA- TAT T-T TAT TAT TAC TAT TAT TAT TAC TAT TA- TAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
4206905 TA- CAT TAAT TTT TAT TAT T-T TCT T-T T-T TAT TGT AAA TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4206947 TAT TAT T-T TAA TAT T-T TAA TAT TA- TAT T-T TAA TAT TTT TCAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
*
4206989 TAT T-T GTAT CAT TAT T-T TCAT TAT T
1 TAT TAT -TAT TAT TAT TAT T-AT TAT T
4207014 TACTCTTATA
Statistics
Matches: 110, Mismatches: 25, Indels: 32
0.66 0.15 0.19
Matches are distributed among these distances:
2 24 0.22
3 78 0.71
4 8 0.07
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4206975 original size:13 final size:13
Alignment explanation
Indices: 4206957--4206982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4206947 TATTATTTTA
4206957 ATATTTTAATATT
1 ATATTTTAATATT
4206970 ATATTTTAATATT
1 ATATTTTAATATT
4206983 TTTCATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTTAATATT
Found at i:4206976 original size:21 final size:22
Alignment explanation
Indices: 4206944--4206984 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
4206934 TTGTAAATAT
4206944 TATTATTATTTTAATATTTTAA
1 TATTATTATTTTAATATTTTAA
4206966 TATTA-TATTTTAATATTTT
1 TATTATTATTTTAATATTTT
4206985 TCATTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATTATTTTAATATTTTAA
Found at i:4206981 original size:8 final size:8
Alignment explanation
Indices: 4206939--4206984 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
4206929 TTTTATTGTA
4206939 AATATTATT
1 AATATT-TT
*
4206948 ATTATTTT
1 AATATTTT
4206956 AATATTTT
1 AATATTTT
4206964 AATA--TT
1 AATATTTT
4206970 -ATATTTT
1 AATATTTT
4206977 AATATTTT
1 AATATTTT
4206985 TCATTATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 2 0.06
8 20 0.62
9 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
AATATTTT
Found at i:4207040 original size:13 final size:12
Alignment explanation
Indices: 4207019--4207062 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
4207009 TTATTTACTC
*
4207019 TTATATATGTCAT
1 TTATTTATGT-AT
4207032 TTATTTATGTAT
1 TTATTTATGTAT
*
4207044 TTATTTATTTATT
1 TTATTTATGTA-T
4207057 TTATTT
1 TTATTT
4207063 TTCGTTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (12 bp):
TTATTTATGTAT
Found at i:4207690 original size:127 final size:127
Alignment explanation
Indices: 4207452--4207679 Score: 293
Period size: 127 Copynumber: 1.8 Consensus size: 127
4207442 AGATAAGATT
*** * *
4207452 TTCTAAAACAAGGCAATGTTTGATGCTCGGAAATTCAGAGAATCGTGCTCTATCGTGCTGGGTTT
1 TTCTAAAACAAGGCAATGTCCAATGCTCGGAAATTCAGAGAATCGTGCCCTACCGTGCTGGGTTT
* * *
4207517 CGATTTCTCGTTTGTCCAAGATAATCGGATATTCCTTTAGAATTTCATTCGTATTCTCTAAA
66 CGATTTCTCGATTGACCAAGATAATCGGACATTCCTTTAGAATTTCATTCGTATTCTCTAAA
* *
4207579 TTCTAAAACAAGGCAATGTCCAATGTTTGGAAATTC-GAGGAATCGTGCCCTACCGTGCTGGGTT
1 TTCTAAAACAAGGCAATGTCCAATGCTCGGAAATTCAGA-GAATCGTGCCCTACCGTGCTGGGTT
* * *
4207643 TCGATTTTTC-ATTGAACTAA-ATAATTGGACA-TCCTTT
65 TCGATTTCTCGATTG-ACCAAGATAATCGGACATTCCTTT
4207680 TGTAATTTTC
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
125 6 0.07
126 14 0.16
127 66 0.77
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (127 bp):
TTCTAAAACAAGGCAATGTCCAATGCTCGGAAATTCAGAGAATCGTGCCCTACCGTGCTGGGTTT
CGATTTCTCGATTGACCAAGATAATCGGACATTCCTTTAGAATTTCATTCGTATTCTCTAAA
Found at i:4212028 original size:11 final size:11
Alignment explanation
Indices: 4212012--4212048 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4212002 GTAATGTTAA
4212012 AATATATACAT
1 AATATATACAT
4212023 AATATATACAT
1 AATATATACAT
4212034 -ATATATA-AT
1 AATATATACAT
4212043 AA-ATAT
1 AATATAT
4212049 TGAAAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 6 0.24
10 8 0.32
11 11 0.44
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATATACAT
Found at i:4227118 original size:31 final size:31
Alignment explanation
Indices: 4227080--4227289 Score: 323
Period size: 31 Copynumber: 6.8 Consensus size: 31
4227070 ACAAATGTCA
* *
4227080 AGTGAAAAGTGGTAGCTCCGGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
4227111 AGTGAAAAATGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
**
4227142 AGTGAAAAGTGGTAGCTTCTCCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
4227173 AGTGAAAAGTGGTAGTTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
4227204 AGTGAAAA-TGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
4227234 AGTGAAAAATGGTAACTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
4227265 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
4227290 AAGTGACAAG
Statistics
Matches: 162, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
30 28 0.17
31 134 0.83
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:4227376 original size:47 final size:47
Alignment explanation
Indices: 4227306--4227430 Score: 162
Period size: 47 Copynumber: 2.7 Consensus size: 47
4227296 CAAGTGATTT
* * *
4227306 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CTGTATAAGACCATATCTAGGATATGGCATCGGTGAGATATATGATA
* * *
4227353 CTGTATAAGACCATATCTAGGATATGGCATCAGTGAGATATGTGATT
1 CTGTATAAGACCATATCTAGGATATGGCATCGGTGAGATATATGATA
* * *
4227400 C-GTGTAAGACCATAGCTAGGCTATGGCATCG
1 CTGTATAAGACCATATCTAGGATATGGCATCG
4227431 ATATATGAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 26 0.38
47 42 0.62
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (47 bp):
CTGTATAAGACCATATCTAGGATATGGCATCGGTGAGATATATGATA
Found at i:4227464 original size:42 final size:43
Alignment explanation
Indices: 4227401--4227515 Score: 146
Period size: 42 Copynumber: 2.7 Consensus size: 43
4227391 TATGTGATTC
* *
4227401 GTGTAAGACCATAGCTAGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
4227443 GTGTAAGACCATAGCTGGGCTATGGTC-TC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGG-CATCGATTATATGAAGAT
* **
4227485 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
4227516 GAAAATGAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.03
42 59 0.94
43 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:4229454 original size:29 final size:30
Alignment explanation
Indices: 4229407--4229474 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
4229397 TGGCCTAAGA
* * *
4229407 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
4229437 GTAAATATAAAAAGTTGAAGGACTAATAGT
1 GTAAATATAAAAAGTTGAAGGACTAATAGT
*
4229467 GCAAATAT
1 GTAAATAT
4229475 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (30 bp):
GTAAATATAAAAAGTTGAAGGACTAATAGT
Found at i:4231946 original size:46 final size:46
Alignment explanation
Indices: 4231894--4232031 Score: 197
Period size: 46 Copynumber: 3.0 Consensus size: 46
4231884 GTGCTCTCTT
*
4231894 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
4231940 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
* * * * * *
4231986 ACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
4232032 TCAAAGATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.01
46 83 0.99
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
Found at i:4233327 original size:20 final size:20
Alignment explanation
Indices: 4233304--4233344 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4233294 AGCTCCACTT
4233304 TGATCTTCGTTCAAATCAAA
1 TGATCTTCGTTCAAATCAAA
4233324 TGATCTTCGTTCAAATCAAA
1 TGATCTTCGTTCAAATCAAA
4233344 T
1 T
4233345 AACAACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TGATCTTCGTTCAAATCAAA
Found at i:4233389 original size:9 final size:9
Alignment explanation
Indices: 4233375--4233400 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4233365 GGCTTGATTC
4233375 ACTGCTGCT
1 ACTGCTGCT
4233384 ACTGCTGCT
1 ACTGCTGCT
4233393 ACTGCTGC
1 ACTGCTGC
4233401 AATGTACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.23, T:0.31
Consensus pattern (9 bp):
ACTGCTGCT
Found at i:4242966 original size:18 final size:18
Alignment explanation
Indices: 4242943--4242979 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4242933 CCTAAGGCCG
4242943 TGCATCTGCTTCTTTTCT
1 TGCATCTGCTTCTTTTCT
4242961 TGCATCTGCTTCTTTTCT
1 TGCATCTGCTTCTTTTCT
4242979 T
1 T
4242980 CTCTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.27, G:0.11, T:0.57
Consensus pattern (18 bp):
TGCATCTGCTTCTTTTCT
Found at i:4242999 original size:26 final size:24
Alignment explanation
Indices: 4242970--4243027 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
4242960 TTGCATCTGC
**
4242970 TTCTTTTCTTCTCTCTTTTTCTTTCT
1 TTCTTTTCTT-TCTAATTTTC-TTCT
4242996 TTCTTTTTCTTTCTAATTTTCTTCT
1 TTC-TTTTCTTTCTAATTTTCTTCT
*
4243021 TTTTTTT
1 TTCTTTT
4243028 TTATTCATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.14
25 6 0.21
26 11 0.39
27 7 0.25
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCTTTTCTTTCTAATTTTCTTCT
Found at i:4243000 original size:14 final size:14
Alignment explanation
Indices: 4242973--4243009 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
4242963 CATCTGCTTC
4242973 TTTTC-TTCTCTCT
1 TTTTCTTTCTCTCT
*
4242986 TTTTCTTTCTTTCT
1 TTTTCTTTCTCTCT
4243000 TTTTCTTTCT
1 TTTTCTTTCT
4243010 AATTTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTCTCTCT
Found at i:4243734 original size:59 final size:58
Alignment explanation
Indices: 4243611--4243734 Score: 128
Period size: 59 Copynumber: 2.1 Consensus size: 58
4243601 GCTCTATTTC
* * * * *
4243611 TTTTTTGGTCATTCAACTATCATTTTTTTTAATTTGATCATCTAACTATTGTACTTTT
1 TTTTTTAGTCACTCAACTATCATTTTTTTTAATTTGATCATCTAACTATTGAAATTGT
*
4243669 TCTTTTTAGTCACTCAACTAT-TTTTTTTTTAAATTTGGA-CATAC-AACTAATTGAAATTGT
1 T-TTTTTAGTCACTCAACTATCATTTTTTTT-AATTT-GATCAT-CTAACT-ATTGAAATTGT
4243729 TTTTTT
1 TTTTTT
4243735 TTTCATTTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
58 9 0.16
59 34 0.62
60 12 0.22
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (58 bp):
TTTTTTAGTCACTCAACTATCATTTTTTTTAATTTGATCATCTAACTATTGAAATTGT
Found at i:4244525 original size:5 final size:5
Alignment explanation
Indices: 4244515--4244553 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
4244505 GTCATTGAAC
4244515 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
4244554 ACTAGAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:4247594 original size:19 final size:20
Alignment explanation
Indices: 4247570--4247608 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
4247560 TCCCATTTTT
4247570 TATTTGTTTTT-TGTTTTAA
1 TATTTGTTTTTATGTTTTAA
4247589 TATTTGTTTTTATGTTTTAA
1 TATTTGTTTTTATGTTTTAA
4247609 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TATTTGTTTTTATGTTTTAA
Found at i:4247626 original size:25 final size:23
Alignment explanation
Indices: 4247570--4247634 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
4247560 TCCCATTTTT
*
4247570 TATTTGTTTTT-TGTTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
*
4247589 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
4247612 TATTTGATTTGTTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
4247635 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 6 0.15
24 3 0.08
25 11 0.28
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:4248460 original size:20 final size:20
Alignment explanation
Indices: 4248435--4248501 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
4248425 GGATATTAAA
4248435 TATTTTAGAAGAATCTTTTT
1 TATTTTAGAAGAATCTTTTT
* ***
4248455 TATTTT-GATATGAATATTAAA
1 TATTTTAGA-A-GAATCTTTTT
4248476 TATTTTAGAAGAATCTTTTT
1 TATTTTAGAAGAATCTTTTT
4248496 TATTTT
1 TATTTT
4248502 TTAATATTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.06
20 19 0.53
21 13 0.36
22 2 0.06
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (20 bp):
TATTTTAGAAGAATCTTTTT
Found at i:4248472 original size:41 final size:41
Alignment explanation
Indices: 4248397--4248501 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 41
4248387 TTTATATGGG
* * *
4248397 TATTTTAGAAG-A--TTTTATATATTGATATGGATATTAAA
1 TATTTTAGAAGAATCTTTTTTATTTTGATATGAATATTAAA
4248435 TATTTTAGAAGAATCTTTTTTATTTTGATATGAATATTAAA
1 TATTTTAGAAGAATCTTTTTTATTTTGATATGAATATTAAA
4248476 TATTTTAGAAGAATCTTTTTTATTTT
1 TATTTTAGAAGAATCTTTTTTATTTT
4248502 TTAATATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
38 11 0.18
39 1 0.02
41 49 0.80
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.52
Consensus pattern (41 bp):
TATTTTAGAAGAATCTTTTTTATTTTGATATGAATATTAAA
Found at i:4248479 original size:21 final size:21
Alignment explanation
Indices: 4248413--4248481 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
4248403 AGAAGATTTT
* *
4248413 ATATATTGATATGGATATTAA
1 ATATTTTGATATGAATATTAA
* **
4248434 ATATTTTAGA-A-GAATCTTTT
1 ATATTTT-GATATGAATATTAA
*
4248454 TTATTTTGATATGAATATTAA
1 ATATTTTGATATGAATATTAA
4248475 ATATTTT
1 ATATTTT
4248482 AGAAGAATCT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 12 0.34
21 19 0.54
22 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (21 bp):
ATATTTTGATATGAATATTAA
Found at i:4250772 original size:20 final size:20
Alignment explanation
Indices: 4250742--4250789 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
4250732 AATTTAGGAT
* * *
4250742 TTTAT-TTTAATTATATTTG
1 TTTATCTTTAATTAAATGTA
4250761 TTTATCTTTAATTAAATGTA
1 TTTATCTTTAATTAAATGTA
4250781 TTTATCTTT
1 TTTATCTTT
4250790 TTAGAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTATCTTTAATTAAATGTA
Found at i:4253916 original size:46 final size:46
Alignment explanation
Indices: 4253864--4254221 Score: 536
Period size: 46 Copynumber: 8.0 Consensus size: 46
4253854 AGTGTGCTCT
4253864 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
4253910 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
4253956 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
4254001 C----ATG---TGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
4254040 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4254086 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * **
4254132 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
4254178 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
4254222 TCACGTCAAA
Statistics
Matches: 290, Mismatches: 13, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
38 34 0.12
39 1 0.00
41 3 0.01
43 3 0.01
45 2 0.01
46 247 0.85
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:4254062 original size:84 final size:85
Alignment explanation
Indices: 4253920--4254181 Score: 409
Period size: 84 Copynumber: 3.0 Consensus size: 85
4253910 CTGATATGAA
4253920 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
4253985 AAAGATACCATGGCAACATG
66 AAAGATACCATGGCAACATG
4254005 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
4254069 AAAGATACCATGGCAACCTGATATGAG
66 AAAGATACCATGGCAA-C----AT--G
* * * **
4254096 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
4254161 AAAGATACCATGGCAACATG
66 AAAGATACCATGGCAACATG
4254181 A
1 A
4254182 CAGAAAATGA
Statistics
Matches: 164, Mismatches: 5, Indels: 16
0.89 0.03 0.09
Matches are distributed among these distances:
84 80 0.49
85 3 0.02
87 2 0.01
89 2 0.01
91 2 0.01
92 75 0.46
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (85 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
AAAGATACCATGGCAACATG
Found at i:4254108 original size:130 final size:131
Alignment explanation
Indices: 4253874--4254221 Score: 529
Period size: 130 Copynumber: 2.6 Consensus size: 131
4253864 CTGATATGAA
4253874 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
4253939 AAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAT
66 AAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAT
4254004 G
131 G
4254005 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
* *
4254069 AAAGATACCATGGCAACCTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGT
66 AAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAT
4254134 G
131 G
* * * *
4254135 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGAC
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAATGTGTAAGAC
* * *
4254199 CATAGTTGAAAGACACTATGGCA
58 CATGGTTGAAAGATACCATGGCA
4254222 TCACGTCAAA
Statistics
Matches: 199, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
130 128 0.64
133 2 0.01
136 1 0.01
137 1 0.01
138 67 0.34
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (131 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
AAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAT
G
Found at i:4254158 original size:176 final size:176
Alignment explanation
Indices: 4253864--4254180 Score: 580
Period size: 176 Copynumber: 1.8 Consensus size: 176
4253854 AGTGTGCTCT
4253864 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
* * **
4253929 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGAAAGATACC
4253994 ATGGCAACATGTGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
131 ATGGCAACATGTGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4254040 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
*
4254105 ACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGAAAGATACC
4254170 ATGGCAACATG
131 ATGGCAACATG
4254181 ACAGAAAATG
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
176 135 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (176 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
ACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGAAAGATACC
ATGGCAACATGTGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:4254527 original size:23 final size:25
Alignment explanation
Indices: 4254482--4254528 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
4254472 AATAAATATA
*
4254482 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
4254507 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
4254529 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:4258187 original size:10 final size:9
Alignment explanation
Indices: 4258170--4258238 Score: 68
Period size: 10 Copynumber: 7.1 Consensus size: 9
4258160 CCAATCTTTC
4258170 TTTTTATTT
1 TTTTTATTT
4258179 TTATTTATTAT
1 TT-TTTATT-T
4258190 TTTCCTT-TTT
1 TTT--TTATTT
4258200 TTTTTATTAT
1 TTTTTATT-T
*
4258210 TTATTATTT
1 TTTTTATTT
4258219 TTTTTATTT
1 TTTTTATTT
4258228 TATTTTATTT
1 T-TTTTATTT
4258238 T
1 T
4258239 AGTTAAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
8 2 0.04
9 14 0.27
10 28 0.55
11 5 0.10
12 2 0.04
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTATTT
Found at i:4258228 original size:27 final size:26
Alignment explanation
Indices: 4258170--4258237 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 26
4258160 CCAATCTTTC
*
4258170 TTTTTATTTTTATTTATTATTTTCCT
1 TTTTTTTTTTTATTTATTATTTTCCT
4258196 TTTTTTTTTATTATTTATTATTTT--T
1 TTTTTTTTT-TTATTTATTATTTTCCT
4258221 TTTATTTTATTTTATTT
1 TTT-TTTT-TTTTATTT
4258238 TAGTTAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
25 4 0.11
26 18 0.47
27 16 0.42
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTTTTTTTATTTATTATTTTCCT
Found at i:4258235 original size:19 final size:19
Alignment explanation
Indices: 4258170--4258238 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 19
4258160 CCAATCTTTC
4258170 TTTTTATTTTTATTTATTAT
1 TTTTTATTTTT-TTTATTAT
4258190 TTTCCTT-TTTTTTTTATTAT
1 TTT--TTATTTTTTTTATTAT
*
4258210 TTATTATTTTTTTTATT-T
1 TTTTTATTTTTTTTATTAT
4258228 TATTTTATTTT
1 T-TTTTATTTT
4258239 AGTTAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
18 4 0.09
19 19 0.44
20 13 0.30
21 5 0.12
22 2 0.05
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTTTTTATTAT
Found at i:4258239 original size:27 final size:27
Alignment explanation
Indices: 4258164--4258239 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
4258154 GGCAACCCAA
4258164 TCTTTCTTTTTATTTT-TATTTATTATTT
1 TCTTT-TTTTTATTTTAT-TTTATTATTT
4258192 TCCTTTTTTTT-TTATTA-TTTATTATTT
1 T-CTTTTTTTTATT-TTATTTTATTATTT
4258219 T-TTTTATTTTATTTTATTTTA
1 TCTTTT-TTTTATTTTATTTTA
4258240 GTTAAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
25 4 0.10
26 7 0.17
27 19 0.45
28 8 0.19
29 4 0.10
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (27 bp):
TCTTTTTTTTATTTTATTTTATTATTT
Found at i:4258454 original size:42 final size:41
Alignment explanation
Indices: 4258345--4258476 Score: 169
Period size: 41 Copynumber: 3.2 Consensus size: 41
4258335 ATCCATGGTA
* *
4258345 CCAAACAGTTCTATTCCAGCCCAAAATGCC-TATCCCTGCTG
1 CCAAACAGTTCTATTCCAGCCCAGAATGCCATAT-CCTGCAG
4258386 CCAAACAGTTCTATTCCAGCCCAGAATGCCATATCTCTGCAG
1 CCAAACAGTTCTATTCCAGCCCAGAATGCCATATC-CTGCAG
* * *
4258428 CCAAACAG-TCTATTCCAGCCCTAGAATCCCCAAAACCTGCAG
1 CCAAACAGTTCTATTCCAGCCC-AGAAT-GCCATATCCTGCAG
4258470 CCAAACA
1 CCAAACA
4258477 CCCCTTTTCA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
41 43 0.52
42 34 0.41
43 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.20
Consensus pattern (41 bp):
CCAAACAGTTCTATTCCAGCCCAGAATGCCATATCCTGCAG
Found at i:4259438 original size:118 final size:118
Alignment explanation
Indices: 4259230--4259442 Score: 381
Period size: 118 Copynumber: 1.8 Consensus size: 118
4259220 TGTTTTCCAT
* *
4259230 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
4259295 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCTGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCTGCTAGCCGA
** *
4259348 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACTGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
4259413 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
4259443 TTGGGTAAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 90 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCTGCTAGCCGA
Found at i:4259599 original size:6 final size:6
Alignment explanation
Indices: 4259590--4259635 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
4259580 AAATTTTAAA
4259590 AAAAAG AAAAA- AAAAAG AAAAAG AAAAA- AAAGAA- AAAGAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAA-AAG AAAAA
4259636 AATACTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.22
6 26 0.70
7 3 0.08
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:4259599 original size:9 final size:9
Alignment explanation
Indices: 4259587--4259637 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
4259577 ATAAAATTTT
4259587 AAAAAAAAG
1 AAAAAAAAG
4259596 AAAAAAAA-
1 AAAAAAAAG
*
4259604 AAGAAAAAG
1 AAAAAAAAG
4259613 AAAAAAAAG
1 AAAAAAAAG
*
4259622 AAAAAGAAG
1 AAAAAAAAG
4259631 AAAAAAA
1 AAAAAAA
4259638 TACTAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
8 7 0.19
9 30 0.81
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:4259610 original size:18 final size:18
Alignment explanation
Indices: 4259587--4259637 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
4259577 ATAAAATTTT
4259587 AAAAAAAAGAAAAAAAA-
1 AAAAAAAAGAAAAAAAAG
*
4259604 AAGAAAAAGAAAAAAAAG
1 AAAAAAAAGAAAAAAAAG
*
4259622 AAAAAGAAGAAAAAAA
1 AAAAAAAAGAAAAAAA
4259638 TACTAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAAG
Found at i:4259616 original size:15 final size:15
Alignment explanation
Indices: 4259598--4259636 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
4259588 AAAAAAAGAA
4259598 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
4259613 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
4259628 AAGAAAAAA
1 AA-AAAAAA
4259637 ATACTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:4262988 original size:19 final size:21
Alignment explanation
Indices: 4262950--4262998 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
4262940 TATATTTATC
4262950 TATACTATATGTTATAAAAAA
1 TATACTATATGTTATAAAAAA
*
4262971 TATACT-TAT-TTTTAAAAAA
1 TATACTATATGTTATAAAAAA
* *
4262990 AATATTATA
1 TATACTATA
4262999 ATTTTTGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.54
20 5 0.21
21 6 0.25
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
TATACTATATGTTATAAAAAA
Found at i:4263002 original size:21 final size:21
Alignment explanation
Indices: 4262965--4263004 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4262955 TATATGTTAT
*
4262965 AAAAAATATACTTATTTTTAA
1 AAAAAATATACTAATTTTTAA
4262986 AAAAAATATTA-TAATTTTT
1 AAAAAATA-TACTAATTTTT
4263005 GTCATATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAAATATACTAATTTTTAA
Found at i:4263299 original size:29 final size:28
Alignment explanation
Indices: 4263249--4263304 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
4263239 TTATATATTT
* *
4263249 ACTTAATTTTAGATTATATCAACCAAAC
1 ACTTAAATTTAGATTATATCAAACAAAC
4263277 ACTTAAATTTAGATT-TCAGTCAAACAAA
1 ACTTAAATTTAGATTAT-A-TCAAACAAA
4263305 ATAAACTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 15 0.62
29 8 0.33
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (28 bp):
ACTTAAATTTAGATTATATCAAACAAAC
Found at i:4267777 original size:21 final size:21
Alignment explanation
Indices: 4267753--4267793 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4267743 TAACGTGTCA
* *
4267753 TTATTACTATTATTTTTATTT
1 TTATTACCATTATTATTATTT
4267774 TTATTACCATTATTATTATT
1 TTATTACCATTATTATTATT
4267794 ATACTTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTACCATTATTATTATTT
Found at i:4267873 original size:3 final size:3
Alignment explanation
Indices: 4267865--4268012 Score: 108
Period size: 3 Copynumber: 48.7 Consensus size: 3
4267855 TATTTCTAAC
* *
4267865 TAT TAT TAT TTT TAT GTAT ATAT TAT TAT T-T ATAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * * * *
4267912 TAC TAT TAT TAAA TAT TCT TAT TAT TAC TAT TAT T-T TAT TCCT T-T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
* * *
4267957 TAT TAT TGTT TAT TAT CAT TA- TAT TAT TAT TAT TACT T-C TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
4268002 TAT TAT TAT TA
1 TAT TAT TAT TA
4268013 CTTTTTTTGT
Statistics
Matches: 114, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
2 8 0.07
3 91 0.80
4 15 0.13
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4268068 original size:3 final size:3
Alignment explanation
Indices: 4268060--4268091 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4268050 TTATTGTTTA
4268060 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4268092 CTATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4268636 original size:25 final size:25
Alignment explanation
Indices: 4268608--4268656 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4268598 ATTTCATTTA
*
4268608 TCATCAT-ATTTATTTCATTTTGTTC
1 TCATCATCA-TTATTTCATTATGTTC
*
4268633 TCATTATCATTATTTCATTATGTT
1 TCATCATCATTATTTCATTATGTT
4268657 TATTCGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.22, C:0.14, G:0.04, T:0.59
Consensus pattern (25 bp):
TCATCATCATTATTTCATTATGTTC
Found at i:4269714 original size:24 final size:26
Alignment explanation
Indices: 4269676--4269725 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
4269666 AATAACGAGA
4269676 ATAAATAAAAGTAAT-ATGTAAAAAAT
1 ATAAATAAAAGTAATGA-GTAAAAAAT
4269702 ATAAAT-AAA-TAATGAGTAAAAAAT
1 ATAAATAAAAGTAATGAGTAAAAAAT
4269726 GTACAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.57
25 4 0.17
26 6 0.26
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (26 bp):
ATAAATAAAAGTAATGAGTAAAAAAT
Found at i:4269733 original size:22 final size:21
Alignment explanation
Indices: 4269708--4269755 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4269698 AAATATAAAT
4269708 AAATAATGAGTAAAAAATGTAC
1 AAATAATGAGT-AAAAATGTAC
* * *
4269730 AAATAATGGGTGAAAATGTAT
1 AAATAATGAGTAAAAATGTAC
4269751 AAATA
1 AAATA
4269756 TGAATAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.25
Consensus pattern (21 bp):
AAATAATGAGTAAAAATGTAC
Found at i:4269790 original size:4 final size:4
Alignment explanation
Indices: 4269776--4269809 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
4269766 AAATATAAGG
*
4269776 TAAA GAAA TAAA TAAA T-AA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
4269810 TAGTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:4269821 original size:15 final size:15
Alignment explanation
Indices: 4269781--4269811 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4269771 TAAGGTAAAG
4269781 AAATAAATAAATAAT
1 AAATAAATAAATAAT
4269796 AAATAAATAAATAAT
1 AAATAAATAAATAAT
4269811 A
1 A
4269812 GTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAATAAATAAT
Found at i:4269969 original size:13 final size:14
Alignment explanation
Indices: 4269953--4269990 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
4269943 GGGTAAATCA
4269953 AAATAAAATAAAT-
1 AAATAAAATAAATG
*
4269966 AAATTAAAT-AATG
1 AAATAAAATAAATG
4269979 AAATAAAATAAA
1 AAATAAAATAAA
4269991 GGACCAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 3 0.14
13 16 0.76
14 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAAAATAAATG
Found at i:4271404 original size:19 final size:19
Alignment explanation
Indices: 4271376--4271413 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4271366 ATACCTAACT
*
4271376 GAATCGATGTCTAAATGAC
1 GAATCAATGTCTAAATGAC
4271395 GAATCAATGTCTAAATGAC
1 GAATCAATGTCTAAATGAC
4271414 TTGTGATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (19 bp):
GAATCAATGTCTAAATGAC
Found at i:4272011 original size:2 final size:2
Alignment explanation
Indices: 4272006--4272030 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4271996 CAGATTTTTT
4272006 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 T
4272031 TTTCAACCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4273413 original size:17 final size:17
Alignment explanation
Indices: 4273387--4273419 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4273377 AATATTTAAT
4273387 TTTAAATTTAGAAAATA
1 TTTAAATTTAGAAAATA
*
4273404 TTTAATTTTAGAAAAT
1 TTTAAATTTAGAAAAT
4273420 TAGGTGGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAGAAAATA
Found at i:4276827 original size:15 final size:15
Alignment explanation
Indices: 4276807--4276850 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4276797 AATAAAGAGT
4276807 AATAATAATAATAAG
1 AATAATAATAATAAG
4276822 AATAATGAA-AATAAG
1 AATAAT-AATAATAAG
* *
4276837 AGTAATATTAATAA
1 AATAATAATAATAA
4276851 TACATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAG
Found at i:4277128 original size:3 final size:3
Alignment explanation
Indices: 4277120--4277148 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4277110 GGATGTGTAT
4277120 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4277149 GGAAATAGTA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4277413 original size:19 final size:19
Alignment explanation
Indices: 4277376--4277414 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4277366 AAATAATCAT
*
4277376 AGTAATAATAATAAGTTAA
1 AGTAATAATAATAAATTAA
4277395 AGTAATAATAA-AATATTAA
1 AGTAATAATAATAA-ATTAA
4277414 A
1 A
4277415 TATGTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (19 bp):
AGTAATAATAATAAATTAA
Found at i:4280980 original size:18 final size:17
Alignment explanation
Indices: 4280945--4280977 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4280935 CTTTTTATTC
4280945 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
4280962 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
4280978 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:4287712 original size:44 final size:43
Alignment explanation
Indices: 4287642--4287799 Score: 156
Period size: 44 Copynumber: 3.6 Consensus size: 43
4287632 ATTTCTAGCT
* *
4287642 TGTTACCCTACTGCATAGGGGTTTAAGGCCCATCGCCTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTC-ATC
* ***** *** *
4287686 TGTTTCCCTACTGCTTAGGGGGTTAAGATTTGT-AAATTCAGCC
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCA-TC
*
4287729 TGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCAATC
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTC-ATC
*
4287773 TGTTTCCCTACTGCTTAGGGGGTTAAG
1 TGTTACCCTACTGCTTAGGGGGTTAAG
4287800 ATCTGTAAAT
Statistics
Matches: 86, Mismatches: 25, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
42 1 0.01
43 30 0.35
44 54 0.63
45 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (43 bp):
TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCATC
Found at i:4287743 original size:43 final size:43
Alignment explanation
Indices: 4287685--4288029 Score: 191
Period size: 43 Copynumber: 8.0 Consensus size: 43
4287675 CGCCTTCGAT
* *
4287685 CTGTTTCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* ** ** *** **
4287728 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTCAGC
* *
4287772 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* ** ** * *
4287815 TTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGT-CTTTGA-T
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATTCAGC
* * * **
4287859 TTGCT-CCACTACTGCTTAGGGAGACAAGATCTGTAAATTCAGC
1 CTGTTACC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
** * *
4287902 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATTCAG-C
* * * * **
4287946 TTGCT-CCACTACTACTTAGGGAGACAAGATCTGTAAATTCAGC
1 CTGTTACC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* * * *
4287989 ATGTTACTCTACTGCTTAGGGGGTTAAGGTCTGTGAATTCA
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCA
4288030 CCGATCTAGG
Statistics
Matches: 215, Mismatches: 70, Indels: 34
0.67 0.22 0.11
Matches are distributed among these distances:
41 4 0.02
42 5 0.02
43 116 0.54
44 81 0.38
45 5 0.02
46 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
Found at i:4287774 original size:87 final size:87
Alignment explanation
Indices: 4287617--4288017 Score: 500
Period size: 87 Copynumber: 4.6 Consensus size: 87
4287607 CAATTTCAGA
* * * * * *
4287617 GAGAAAAGATTTGTAATTTCTAGCTTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCGCCTTC
1 GAGACAAGATCTGTAAATTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTC
*
4287682 GATCTGTTTCC-CTACTGCTTAGG
65 GATCTG-CTCCACTACTGCTTAGG
* ** * * *
4287705 GGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCA
1 GAGACAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
*
4287770 ATCTGTTTCC-CTACTGCTTAGG
66 ATCTG-CTCCACTACTGCTTAGG
* ** * * * * *
4287792 GGGTTAAGATCTGTAAATTTAGCTTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTG
1 GAGACAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
*
4287857 ATTTGCTCCACTACTGCTTAGG
66 ATCTGCTCCACTACTGCTTAGG
* *
4287879 GAGACAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCG
1 GAGACAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
* *
4287944 ATTTGCTCCACTACTACTTAGG
66 ATCTGCTCCACTACTGCTTAGG
* *
4287966 GAGACAAGATCTGTAAATTCAGCATGTTACTCTACTGCTTAGGGGGTTAAGG
1 GAGACAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
4288018 TCTGTGAATT
Statistics
Matches: 286, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
86 3 0.01
87 267 0.93
88 16 0.06
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (87 bp):
GAGACAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
ATCTGCTCCACTACTGCTTAGG
Found at i:4292794 original size:47 final size:45
Alignment explanation
Indices: 4292720--4292848 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 45
4292710 AAATTGAGAT
* *
4292720 CCGAACTCGTTGAGCTGCGTTCTGAGTTCACCTATGGATGC-AAGCA
1 CCGAACTCGTTGAGTTGCGTTCCGAGTTCA-CTATGGATGCGAA-CA
* * *
4292766 TTCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGCGAACA
1 -CCGAACTCGTTGAGTTGCGTTCCGAGTTCACTATGGATGCGAACA
* * *
4292812 CCTGAGCTCGTTGAGTTGCATTCCGAGTTCATTATGG
1 CC-GAACTCGTTGAGTTGCGTTCCGAGTTCACTATGG
4292849 GTGAGATTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
45 1 0.01
46 42 0.59
47 28 0.39
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGCGTTCCGAGTTCACTATGGATGCGAACA
Found at i:4295742 original size:20 final size:20
Alignment explanation
Indices: 4295705--4295744 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4295695 AAGATTAATA
*
4295705 TGATATTTATTTTCATACAT
1 TGATATTTATTATCATACAT
4295725 TGATATTTATATAT-ATACAT
1 TGATATTTAT-TATCATACAT
4295745 AATTTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (20 bp):
TGATATTTATTATCATACAT
Found at i:4297982 original size:15 final size:16
Alignment explanation
Indices: 4297959--4297992 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4297949 ATTTTAATTT
*
4297959 AAAATTTAATAA-GAA
1 AAAAATTAATAATGAA
4297974 AAAAATTAATAATGAA
1 AAAAATTAATAATGAA
4297990 AAA
1 AAA
4297993 GGAAATGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAAATTAATAATGAA
Found at i:4299415 original size:56 final size:58
Alignment explanation
Indices: 4299296--4299415 Score: 140
Period size: 56 Copynumber: 2.1 Consensus size: 58
4299286 CTCTATTTCT
* * * *
4299296 TTTTTAGTCACTCAACTATTATTTTTTTAATTTGATCATCTAACTATTGTACTTTTTCT
1 TTTTTAGTCACTCAAC-ATTATTTTTTTAATTTGATCATCTAACTATTGAAATTATTCA
*
4299355 TTTTTGGTCACTCAAC-TT-TTTTTTTAATTTGATCATAC-AACTAATTGAAATTATT-A
1 TTTTTAGTCACTCAACATTATTTTTTTAATTTGATCAT-CTAACT-ATTGAAATTATTCA
4299411 TTTTT
1 TTTTT
4299416 TCATTTCCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
56 27 0.50
57 12 0.22
59 15 0.28
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (58 bp):
TTTTTAGTCACTCAACATTATTTTTTTAATTTGATCATCTAACTATTGAAATTATTCA
Found at i:4299604 original size:14 final size:14
Alignment explanation
Indices: 4299585--4299617 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4299575 ATGGCACTTG
4299585 ACAAAAATATACCA
1 ACAAAAATATACCA
4299599 ACAAAAATATACCA
1 ACAAAAATATACCA
4299613 A-AAAA
1 ACAAAA
4299618 GAAAATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (14 bp):
ACAAAAATATACCA
Found at i:4309107 original size:9 final size:10
Alignment explanation
Indices: 4309082--4309110 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
4309072 ATCATTTTAA
4309082 TTAAAAAATT
1 TTAAAAAATT
4309092 TTAAAAAATT
1 TTAAAAAATT
4309102 TTAAAAAAT
1 TTAAAAAAT
4309111 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:4310204 original size:2 final size:2
Alignment explanation
Indices: 4310197--4310239 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
4310187 AATGTATGGA
** *
4310197 AT AT AT AT AT AT AT AT AT AT AT AT -T CC AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4310238 AT
1 AT
4310240 TGATGTGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4313469 original size:20 final size:20
Alignment explanation
Indices: 4313433--4313472 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4313423 TCCTATTGTT
4313433 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
4313453 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
4313473 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:4314393 original size:44 final size:44
Alignment explanation
Indices: 4314334--4314628 Score: 195
Period size: 44 Copynumber: 6.9 Consensus size: 44
4314324 TAGTGTCTTC
*
4314334 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTATTTT
* * * * * * *
4314378 AATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATAGT-GT-CTTC
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTTATTTT
* *
4314421 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTAATTCTTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTA-T-TTT
* * * **
4314467 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA-C-CTGA-CGT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTATTTT
* * * *
4314508 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAAATC-C----TTT
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTTATTTT
* * * * * *
4314547 AATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-TAC-TATCCTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-CTTAT-TTT
*
4314591 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT
4314629 GGCTTTAGTT
Statistics
Matches: 186, Mismatches: 47, Indels: 35
0.69 0.18 0.13
Matches are distributed among these distances:
39 24 0.13
40 3 0.02
41 26 0.14
42 3 0.02
43 31 0.17
44 64 0.34
45 3 0.02
46 32 0.17
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTATTTT
Found at i:4314405 original size:87 final size:84
Alignment explanation
Indices: 4314251--4314628 Score: 353
Period size: 87 Copynumber: 4.5 Consensus size: 84
4314241 AGACTTGATG
* * * * * *
4314251 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-C-TTTAATCCACTCCACTGTAA-CTTCG
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAATC-TCA
*
4314313 GGGAGATAGGATAGTGTCTT
65 GGGAGATAGGATACTGTCTT
4314333 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTGTAA-CT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC---TTTTAATCCGCTCCACTGTAATC-
*
4314397 TCAGGGAGATAGGATAGTGTCTT
62 TCAGGGAGATAGGATACTGTCTT
** * *
4314420 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTAATTCTTTGGTCTGTTCCACTGTAAT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC----T-TTTAATCCGCTCCACTGTAAT
* * * *
4314485 CTCAGGGAGATAAGA-CCTGACGT
61 CTCAGGGAGATAGGATACTGTCTT
* ** * * *
4314508 -GATCTTCTCTACTGTAA-CTTCAGAGAGATAAAATC-C-TTTAATCCGCTCCATTGTAATCTCA
1 CGATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAATCTCA
* *
4314569 AGGAGATAGGATTACTATCCTT
65 GGGAGATAGGA-TACTGT-CTT
4314591 -GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
4314629 GGCTTTAGTT
Statistics
Matches: 242, Mismatches: 39, Indels: 27
0.79 0.13 0.09
Matches are distributed among these distances:
80 29 0.12
82 34 0.14
83 31 0.13
84 2 0.01
86 2 0.01
87 109 0.45
88 5 0.02
89 29 0.12
90 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (84 bp):
CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAATCTCAG
GGAGATAGGATACTGTCTT
Found at i:4314909 original size:86 final size:87
Alignment explanation
Indices: 4314803--4315143 Score: 353
Period size: 86 Copynumber: 4.0 Consensus size: 87
4314793 AATCTATAAC
* * * *
4314803 CTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTA
1 CTTTAACCAGCTCC-ATGCAACCGATAGAGGCAAGGCTTTGTGTCTTCGATCTGCTTCGCTGTCA
4314866 ATGCAGGAAGGCAAGATCTGCTTT
65 ATGCAGGAAGGCAAGATCT-CTTT
* * * * * *
4314890 -TTTAACTAGCTCCACTGCAATCGATGGACGCAAAGCTTTGT-T-TTCGATCTGCTTCGCTGTTA
1 CTTTAACCAGCTCCA-TGCAACCGATAGAGGCAAGGCTTTGTGTCTTCGATCTGCTTCGCTGTCA
*
4314952 ATGTAGGAAGGCAAGATC-CTTTGT
65 ATGCAGGAAGGCAAGATCTC-TT-T
* * * * *
4314976 CTTCAACCAGCTCTATCACAACCGA-AGAGGCAAGGTTTTGTGTCTTCGATCTGCTTTGCTGTCA
1 CTTTAACCAGCTCCAT-GCAACCGATAGAGGCAAGGCTTTGTGTCTTCGATCTGCTTCGCTGTCA
* * *
4315040 ATGCAGAAAAGCAAGATCTTTTGT
65 ATGCAGGAAGGCAAGATCTCTT-T
*
4315064 CTTTAACCAGCAT-CA--CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCA
1 CTTTAACCAGC-TCCATGCAACCGATAGAGGCAAGGCTTTGTGTCTTCGATCTGCTTCGCTGTCA
4315125 ATGCAGGAAGGCAAGATCT
65 ATGCAGGAAGGCAAGATCT
4315144 GTAACTTCAT
Statistics
Matches: 217, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
84 1 0.00
85 54 0.25
86 95 0.44
87 18 0.08
88 48 0.22
89 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (87 bp):
CTTTAACCAGCTCCATGCAACCGATAGAGGCAAGGCTTTGTGTCTTCGATCTGCTTCGCTGTCAA
TGCAGGAAGGCAAGATCTCTTT
Found at i:4315122 original size:85 final size:87
Alignment explanation
Indices: 4314932--4315143 Score: 322
Period size: 85 Copynumber: 2.4 Consensus size: 87
4314922 AAGCTTTGTT
* * *
4314932 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCCTTTGTCTTCAACCAGCTCTATCACAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGC-CTATCACAA
4314997 CCGAAGAGGCAAGGTTTTGTGTC
65 CCGAAGAGGCAAGGTTTTGTGTC
* * * *
4315020 TTCGATCTGCTTTGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTTAACCAG-C-ATCACAAC
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCCTATCACAAC
4315083 CGAAAGAGGCAAGG-TTTGTGTC
66 CG-AAGAGGCAAGGTTTTGTGTC
4315105 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
4315144 GTAACTTCAT
Statistics
Matches: 113, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
85 54 0.48
86 12 0.11
88 47 0.42
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCCTATCACAAC
CGAAGAGGCAAGGTTTTGTGTC
Found at i:4316393 original size:1 final size:1
Alignment explanation
Indices: 4316387--4316420 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
4316377 AAAGTTCCTC
*
4316387 TTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4316421 AGAGCAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:4316404 original size:14 final size:14
Alignment explanation
Indices: 4316385--4316420 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4316375 CCAAAGTTCC
4316385 TCTTTTTTTTTTTT
1 TCTTTTTTTTTTTT
4316399 TCTTTTTTTTTTTT
1 TCTTTTTTTTTTTT
4316413 T-TTTTTTT
1 TCTTTTTTT
4316421 AGAGCAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (14 bp):
TCTTTTTTTTTTTT
Found at i:4328806 original size:20 final size:20
Alignment explanation
Indices: 4328770--4328809 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4328760 TCCTATTGTT
4328770 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
4328790 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
4328810 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:4334295 original size:18 final size:16
Alignment explanation
Indices: 4334263--4334304 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
4334253 ATTTACATAT
4334263 TTATATTAT-ATTATAAA
1 TTATATT-TGATTAT-AA
4334280 TTATCATTTGATTATAA
1 TTAT-ATTTGATTATAA
4334297 TTATATTT
1 TTATATTT
4334305 ATATAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
TTATATTTGATTATAA
Found at i:4347806 original size:35 final size:35
Alignment explanation
Indices: 4347760--4347831 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4347750 AAGGTAACCC
4347760 ATAAAGCTACTAGTTTCCAGAAATGGTTTTGGACT
1 ATAAAGCTACTAGTTTCCAGAAATGGTTTTGGACT
4347795 ATAAAGCTACTAGTTTCCAGAAATGGTTTTGGACT
1 ATAAAGCTACTAGTTTCCAGAAATGGTTTTGGACT
4347830 AT
1 AT
4347832 CTTCGGCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (35 bp):
ATAAAGCTACTAGTTTCCAGAAATGGTTTTGGACT
Found at i:4358179 original size:15 final size:15
Alignment explanation
Indices: 4358159--4358193 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4358149 ATTTTAATAA
* *
4358159 TTAAATTTACATTTT
1 TTAAATTTAAAATTT
4358174 TTAAATTTAAAATTT
1 TTAAATTTAAAATTT
4358189 TTAAA
1 TTAAA
4358194 AAATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAATTTAAAATTT
Found at i:4359710 original size:27 final size:25
Alignment explanation
Indices: 4359647--4359849 Score: 123
Period size: 24 Copynumber: 7.9 Consensus size: 25
4359637 CCAAAATATT
* * *
4359647 ATAT-AAAACAATTTGAAGTCAATA
1 ATATCAAAACAATTTAAAATAAATA
* *
4359671 ATAT-AAAACAATTTCAAGTAAATA
1 ATATCAAAACAATTTAAAATAAATA
4359695 ATATGCAAAACAAATTTAAAATAAATA
1 ATAT-CAAAAC-AATTTAAAATAAATA
*
4359722 ATATACAAAACAATTTAAAATGAATA
1 ATAT-CAAAACAATTTAAAATAAATA
* *
4359748 ATAT-ATAAGACACTTTAAAAT-AA-C
1 ATATCA-AA-ACAATTTAAAATAAATA
* * *
4359772 ATAT-AAAAGAGTTTAAGATAAATA
1 ATATCAAAACAATTTAAAATAAATA
*
4359796 ATA-CGGAAAAAGAAATTTAAAATAAATA
1 ATATC---AAAA-CAATTTAAAATAAATA
* *
4359824 ATGTACAAAAACAGTTTAAAAATAAA
1 ATAT-C-AAAACAATTT-AAAATAAA
4359850 ATATATATAT
Statistics
Matches: 146, Mismatches: 18, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
22 9 0.06
23 4 0.03
24 35 0.24
25 4 0.03
26 34 0.23
27 31 0.21
28 28 0.19
30 1 0.01
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (25 bp):
ATATCAAAACAATTTAAAATAAATA
Found at i:4359747 original size:26 final size:26
Alignment explanation
Indices: 4359640--4359906 Score: 138
Period size: 27 Copynumber: 10.2 Consensus size: 26
4359630 ATATGCACCA
* * * *
4359640 AAATATTATATAAAACAATTTGAAGT
1 AAATAATATACAAAACAATTTAAAAT
* * *
4359666 CAATAATAT--AAAACAATTTCAAGT
1 AAATAATATACAAAACAATTTAAAAT
*
4359690 AAATAATATGCAAAACAAATTTAAAAT
1 AAATAATATACAAAAC-AATTTAAAAT
4359717 AAATAATATACAAAACAATTTAAAAT
1 AAATAATATACAAAACAATTTAAAAT
* * * *
4359743 GAATAATATATAAGACACTTTAAAAT
1 AAATAATATACAAAACAATTTAAAAT
* * * *
4359769 -AA-CATAT--AAAAGAGTTTAAGAT
1 AAATAATATACAAAACAATTTAAAAT
* *
4359791 AAATAATACGGA-AAAAGAAATTTAAAAT
1 AAATAATA--TACAAAA-CAATTTAAAAT
* *
4359819 AAATAATGTACAAAAACAGTTTAAAAAT
1 AAATAATATAC-AAAACAATTT-AAAAT
* * **
4359847 AAAATATATATA-TAAATAATAAAAAAT
1 -AAATA-ATATACAAAACAATTTAAAAT
* * *
4359874 GAATGATATATATAAAA-AGTTTAAAAT
1 AAAT-A-ATATACAAAACAATTTAAAAT
4359901 AAATAA
1 AAATAA
4359907 CATTTAAAAT
Statistics
Matches: 188, Mismatches: 37, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
22 11 0.06
23 2 0.01
24 29 0.15
25 3 0.02
26 49 0.26
27 53 0.28
28 32 0.17
29 5 0.03
30 4 0.02
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.28
Consensus pattern (26 bp):
AAATAATATACAAAACAATTTAAAAT
Found at i:4359831 original size:102 final size:101
Alignment explanation
Indices: 4359671--4359856 Score: 252
Period size: 102 Copynumber: 1.8 Consensus size: 101
4359661 GAAGTCAATA
* *
4359671 ATATAAAACAATTTCAAGTAAATAATATGCAAAACAAATTTAAAATAAATAATATAC-AAAACAA
1 ATATAAAACAATTTCAAGTAAATAATAGGAAAAACAAATTTAAAATAAATAATATACAAAAACAA
4359735 TTT-AAAATGAATAATATATAAGACACTTTAAAATAAC
66 TTTAAAAAT-AA-AATATATAAGACACTTTAAAATAAC
* * * *
4359772 ATATAAAAGAGTTT-AAGATAAATAATACGGAAAAAGAAATTTAAAATAAATAATGTACAAAAAC
1 ATATAAAACAATTTCAAG-TAAATAATA-GGAAAAACAAATTTAAAATAAATAATATACAAAAAC
*
4359836 AGTTTAAAAATAAAATATATA
64 AATTTAAAAATAAAATATATA
4359857 TATAAATAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
100 3 0.04
101 21 0.28
102 34 0.46
103 11 0.15
104 5 0.07
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (101 bp):
ATATAAAACAATTTCAAGTAAATAATAGGAAAAACAAATTTAAAATAAATAATATACAAAAACAA
TTTAAAAATAAAATATATAAGACACTTTAAAATAAC
Found at i:4359967 original size:26 final size:25
Alignment explanation
Indices: 4359936--4360026 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
4359926 TGATAATAGT
* *
4359936 TTAAAATACATAATATGTGAAAAAC
1 TTAAAATAAATAATATATGAAAAAC
*
4359961 TTAAAA-ATAATAATA-AT-AAAACAGT
1 TTAAAATA-AATAATATATGAAAA-A-C
*
4359986 TTAAAATAAATAATATAAGAAAAAAC
1 TTAAAATAAATAATATATG-AAAAAC
4360012 TTAAAATAAATAATA
1 TTAAAATAAATAATA
4360027 ATAACAAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
23 4 0.07
24 3 0.06
25 25 0.46
26 17 0.31
27 1 0.02
28 4 0.07
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (25 bp):
TTAAAATAAATAATATATGAAAAAC
Found at i:4359981 original size:22 final size:24
Alignment explanation
Indices: 4359956--4360030 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
4359946 TAATATGTGA
4359956 AAAAC-TTAAAAAT-AATAATAAT
1 AAAACATTAAAAATAAATAATAAT
* *
4359978 AAAACAGTTTAAAATAAATAATATAAG
1 AAAACA-TTAAAAATAAAT-A-ATAAT
*
4360005 AAAAAACTT-AAAATAAATAATAAT
1 AAAACA-TTAAAAATAAATAATAAT
4360029 AA
1 AA
4360031 CAAAACAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 5 0.12
24 13 0.30
25 4 0.09
26 10 0.23
27 11 0.26
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (24 bp):
AAAACATTAAAAATAAATAATAAT
Found at i:4359992 original size:50 final size:53
Alignment explanation
Indices: 4359933--4360046 Score: 153
Period size: 50 Copynumber: 2.2 Consensus size: 53
4359923 ACTTGATAAT
* ** *
4359933 AGTTTAAAATACATAATATGTG-AAAAACTT-AA-AAATAATAATAATAAAAC
1 AGTTTAAAATAAATAATATAAGAAAAAACTTAAATAAATAATAATAACAAAAC
4359983 AGTTTAAAATAAATAATATAAGAAAAAACTTAAAATAAATAATAATAACAAAAC
1 AGTTTAAAATAAATAATATAAGAAAAAACTT-AAATAAATAATAATAACAAAAC
4360037 AGTTTTAAAA
1 AG-TTTAAAA
4360047 AAACGAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
50 19 0.35
51 8 0.15
53 2 0.04
54 19 0.35
55 7 0.13
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (53 bp):
AGTTTAAAATAAATAATATAAGAAAAAACTTAAATAAATAATAATAACAAAAC
Found at i:4361765 original size:132 final size:132
Alignment explanation
Indices: 4361526--4361864 Score: 412
Period size: 132 Copynumber: 2.6 Consensus size: 132
4361516 ATTCAATCCA
* * * * ** *
4361526 CTCCACTGCAACTTTAGGGAGATTAG-TCTTGTAGCTTCAATCTTCTTTACTGCAACTTCAGGAA
1 CTCCACTGCAACTTTAGGGAGATAAGAT-TTGTGGCTTAAATCTGCTCCACTGCAACTTCAGGGA
* *** * *
4361590 GATAAGATTTGTGGCATCAACCTACTCCACTGCAACTTTAGGGAGATAAGGTTTGTGGTT-TTAC
65 GATAAGATTCGCCACATCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGTTCTAAC
4361654 TCTG
130 -CTG
* *
4361658 CTCCACTGCAACTTTAGGGAGATAAGATTAGTGGCTTAAATCTGCTCCACTACAACTTCAGGGAG
1 CTCCACTGCAACTTTAGGGAGATAAGATTTGTGGCTTAAATCTGCTCCACTGCAACTTCAGGGAG
* * *
4361723 ATAAGATTCGCCACTTCAACCTGCTCCAGTGCAACTTCAGGGAGATAAGGTTTGTGGTTCTAACC
66 ATAAGATTCGCCACATCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGTTCTAACC
4361788 TG
131 TG
* * * * * * * *
4361790 CTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGTTCCGCTGTAATTTCAAGGAG
1 CTCCACTGCAACTTTAGGGAGATAAGATTTGTGGCTTAAATCTGCTCCACTGCAACTTCAGGGAG
4361855 ATAAGATTCG
66 ATAAGATTCG
4361865 TTATAGTGAT
Statistics
Matches: 177, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
132 173 0.98
133 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (132 bp):
CTCCACTGCAACTTTAGGGAGATAAGATTTGTGGCTTAAATCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTCGCCACATCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGTTCTAACC
TG
Found at i:4361839 original size:44 final size:44
Alignment explanation
Indices: 4361526--4361862 Score: 320
Period size: 44 Copynumber: 7.7 Consensus size: 44
4361516 ATTCAATCCA
* * * * * *
4361526 CTCCACTGCAACTTTAGGGAGATTAG-TCTTGTAGCTTCAATCTT
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TTGTGGCTTTAACCTG
** * * * *
4361570 CTTTACTGCAACTTCAGGAAGATAAGATTTGTGGCATCAACCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAACCTG
* * *
4361614 CTCCACTGCAACTTTAGGGAGATAAGGTTTGTGG-TTTTACTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAAC-CTG
* * * *
4361658 CTCCACTGCAACTTTAGGGAGATAAGATTAGTGGCTTAAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAACCTG
* * *** *
4361702 CTCCACTACAACTTCAGGGAGATAAGATTCGCCACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAACCTG
* *
4361746 CTCCAGTGCAACTTCAGGGAGATAAGGTTTGTGG-TTCTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTT-TAACCTG
* *
4361790 CTCCGCTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAACCTG
* * * * *
4361834 TTCCGCTGTAATTTCAAGGAGATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
4361863 CGTTATAGTG
Statistics
Matches: 241, Mismatches: 47, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
43 5 0.02
44 230 0.95
45 6 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAACCTG
Found at i:4362378 original size:19 final size:17
Alignment explanation
Indices: 4362365--4362401 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4362355 TTTAGTTTTG
4362365 TGGG-CTAGGGTTAGTT
1 TGGGCCTAGGGTTAGTT
*
4362381 TGGGCCTAGGGTTAATT
1 TGGGCCTAGGGTTAGTT
4362398 TGGG
1 TGGG
4362402 TTTGTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.14, C:0.08, G:0.43, T:0.35
Consensus pattern (17 bp):
TGGGCCTAGGGTTAGTT
Found at i:4362414 original size:12 final size:12
Alignment explanation
Indices: 4362392--4362427 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
4362382 GGGCCTAGGG
4362392 TTAATTTGGGTT
1 TTAATTTGGGTT
4362404 TGTAA-TTGGGTT
1 T-TAATTTGGGTT
4362416 TTAATTTGGGTT
1 TTAATTTGGGTT
4362428 ATTTGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 16 0.73
13 3 0.14
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (12 bp):
TTAATTTGGGTT
Found at i:4366172 original size:46 final size:46
Alignment explanation
Indices: 4366112--4366461 Score: 446
Period size: 46 Copynumber: 8.0 Consensus size: 46
4366102 TTTGACGTGA
* * * * * *
4366112 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
4366158 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
4366204 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4366250 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
4366296 TGCCATGGTATCTTTCAATCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4366334 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4366380 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
4366418 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
4366462 AGAGCACACT
Statistics
Matches: 270, Mismatches: 17, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
38 65 0.24
39 2 0.01
40 6 0.02
41 2 0.01
43 2 0.01
44 6 0.02
45 6 0.02
46 181 0.67
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:4366228 original size:92 final size:84
Alignment explanation
Indices: 4366156--4366461 Score: 477
Period size: 84 Copynumber: 3.5 Consensus size: 84
4366146 TTTCTGTCAT
** * * *
4366156 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
4366221 ACCATGGTCTTACACATCTCATATCAG
66 ACCATGGTCTT--ACA---C--A-CAG
*
4366248 ATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
*
4366313 ATCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
4366332 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
4366397 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
4366416 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
4366462 AGAGCACACT
Statistics
Matches: 205, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
84 131 0.64
85 1 0.00
87 1 0.00
90 3 0.01
92 69 0.34
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (84 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
ACCATGGTCTTACACACAG
Found at i:4366342 original size:38 final size:38
Alignment explanation
Indices: 4366291--4366450 Score: 239
Period size: 38 Copynumber: 4.0 Consensus size: 38
4366281 CATTTCATAT
*
4366291 CAGGTTGCCATGGTATCTTTCAATCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
4366329 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
4366374 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
4366413 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
4366451 TTTCATATCA
Statistics
Matches: 113, Mismatches: 1, Indels: 16
0.87 0.01 0.12
Matches are distributed among these distances:
38 70 0.62
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 33 0.29
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:4370747 original size:5 final size:5
Alignment explanation
Indices: 4370737--4370764 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4370727 TATATGATTA
4370737 ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATA
4370765 ACATAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:4371149 original size:18 final size:19
Alignment explanation
Indices: 4371111--4371149 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4371101 TCAAAATGGA
*
4371111 TTATTTTAAATTTTTAAAT
1 TTATTTTAAATTTATAAAT
*
4371130 TTATTTT-AATTTATATAT
1 TTATTTTAAATTTATAAAT
4371148 TT
1 TT
4371150 TGATTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTAAATTTATAAAT
Found at i:4382513 original size:18 final size:19
Alignment explanation
Indices: 4382471--4382513 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4382461 AAATTTTCTA
**
4382471 TTTCATTCAAACAAGTAGT
1 TTTCATTCAAACAAGTAAC
*
4382490 TTTCATTCACACAA-TAAC
1 TTTCATTCAAACAAGTAAC
4382508 TTTCAT
1 TTTCAT
4382514 ATAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTCATTCAAACAAGTAAC
Found at i:4383763 original size:27 final size:25
Alignment explanation
Indices: 4383730--4383791 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
4383720 ATTTACTATA
4383730 TTTTTATATAGT-ATTAATAAATATTT
1 TTTTTATATAGTAATT--TAAATATTT
*
4383756 TTGTTTATCA-AGTAATTTAAATGTTT
1 TT-TTTAT-ATAGTAATTTAAATATTT
4383782 TTTTTATATA
1 TTTTTATATA
4383792 TTTTTATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
24 1 0.03
25 6 0.19
26 12 0.39
27 8 0.26
28 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTTTATATAGTAATTTAAATATTT
Found at i:4386011 original size:39 final size:39
Alignment explanation
Indices: 4385920--4386189 Score: 454
Period size: 39 Copynumber: 7.0 Consensus size: 39
4385910 ATTATATTAT
* *
4385920 CAGCACAAAGCCTGCGGGACTTTA-ACCGGATACATTT-
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
4385957 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
4385996 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
4386035 CAGCACGAAGCCTGCGGGACTTTAGTCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * *
4386074 CAGCACGAAGCCTGTGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
4386113 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
4386152 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
4386190 TAGTGTCTTG
Statistics
Matches: 219, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
37 22 0.10
38 12 0.05
39 185 0.84
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:4388136 original size:5 final size:5
Alignment explanation
Indices: 4388126--4388163 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
4388116 TTCATTTTTC
4388126 TTCTT TTC-T TTCTT TTCTTT TTCTT TTCTTT TTCTT TT
1 TTCTT TTCTT TTCTT TTC-TT TTCTT TTC-TT TTCTT TT
4388164 TGTTGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.13
5 16 0.53
6 10 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTCTT
Found at i:4388149 original size:6 final size:6
Alignment explanation
Indices: 4388114--4388164 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
4388104 TTAGTTTAGG
*
4388114 TTTTCAT TTTTCT TCTTT-T CTTTC- TTTTCT TTTTC- TTTTCT TTTTCT
1 TTTTC-T TTTTCT T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
4388161 TTTT
1 TTTT
4388165 GTTGTTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 12 0.32
6 18 0.47
7 8 0.21
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:4388150 original size:11 final size:11
Alignment explanation
Indices: 4388114--4388163 Score: 66
Period size: 11 Copynumber: 4.4 Consensus size: 11
4388104 TTAGTTTAGG
4388114 TTTTCATTTTTC
1 TTTTC-TTTTTC
4388126 TTCTT-TTCTTTC
1 TT-TTCTT-TTTC
4388138 TTTTCTTTTTC
1 TTTTCTTTTTC
4388149 TTTTCTTTTTC
1 TTTTCTTTTTC
4388160 TTTT
1 TTTT
4388164 TGTTGTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 23 0.66
12 10 0.29
13 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:4389281 original size:19 final size:21
Alignment explanation
Indices: 4389253--4389299 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
4389243 AATTATGATT
4389253 TATAAATTTA-TT-TTAACAC
1 TATAAATTTACTTATTAACAC
*
4389272 TATAACTTTACTTATTAACA-
1 TATAAATTTACTTATTAACAC
*
4389292 TGTAAATT
1 TATAAATT
4389300 GTAATAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (21 bp):
TATAAATTTACTTATTAACAC
Found at i:4392186 original size:36 final size:38
Alignment explanation
Indices: 4392131--4392204 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 38
4392121 TAGTATTACA
4392131 CTCAACTTTAACAATGCTTAA-AGATAT-AAAAAGTTGG
1 CTCAACTTTAACAATGCTTAATA-ATATAAAAAAGTTGG
4392168 CTCAACTTT-ACAATGCTTAATAATATACAAAAAGTTG
1 CTCAACTTTAACAATGCTTAATAATATA-AAAAAGTTG
4392205 TCTCGATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 15 0.44
37 10 0.29
38 9 0.26
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (38 bp):
CTCAACTTTAACAATGCTTAATAATATAAAAAAGTTGG
Found at i:4394731 original size:15 final size:15
Alignment explanation
Indices: 4394711--4394741 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4394701 TTTCTCTTGA
4394711 AATAAGTATTTAGTC
1 AATAAGTATTTAGTC
4394726 AATAAGTATTTAGTC
1 AATAAGTATTTAGTC
4394741 A
1 A
4394742 TTAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (15 bp):
AATAAGTATTTAGTC
Found at i:4395521 original size:48 final size:47
Alignment explanation
Indices: 4395371--4395732 Score: 293
Period size: 48 Copynumber: 7.6 Consensus size: 47
4395361 GGTAAAATAC
* * * ** **
4395371 CGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATAACAATAC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTC-TCATAA-TGTGG
* * * * * *
4395419 CGATGCCATGTTCCAAGCATGATCTTACACTGGC-CGCATATTGAGG
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
* *
4395465 CCGATGCCATATCCCAAACATGGTCTTACATTGGCTCTCATAATGTGG
1 -CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
* * * * *
4395513 CAGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAAGT--
1 C-GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTC--AT-AATGTGG
* *
4395562 CGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCATAATGTGG
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
* * * * * ****
4395609 TCGATGCCATGTCTCAGACATGGTCTTACACTAGCACACAT-ATCAACAC
1 -CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAT--GTGG
*
4395658 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATATGG
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
*
4395705 CCGATGCCATGTCCCAAATATGGTCTTA
1 -CGATGCCATGTCCCAAACATGGTCTTA
4395733 TGTTAGCACA
Statistics
Matches: 250, Mismatches: 50, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
45 4 0.02
46 2 0.01
47 37 0.15
48 198 0.79
49 3 0.01
50 2 0.01
51 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
Found at i:4395589 original size:96 final size:95
Alignment explanation
Indices: 4395369--4395751 Score: 432
Period size: 96 Copynumber: 4.0 Consensus size: 95
4395359 AGGGTAAAAT
* * * ** ** *
4395369 ACCGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATAACAATACCGATGCCATGTTCC
1 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTC-TCATAA-TGTGGCGATGCCATGTCCC
* * * ** *
4395433 A-AGCATGATCTTACACTGGC-CGCATATTGAG
64 AGA-CATGGTCTTACACTAGCACACATATCAAC
* * *
4395464 GCCGATGCCATATCCCAAACATGGTCTTACATTGGCTCTCATAATGTGGCAGATGCCATGTCCCA
1 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGC-GATGCCATGTCCCA
4395529 GACATGGTCTTACACTAGCACACATATCAA-
65 GACATGGTCTTACACTAGCACACATATCAAC
* * * *
4395559 AGTCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCATAATGTGGTCGATGCCATGTCTC
1 A-CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG-CGATGCCATGTCCC
4395624 AGACATGGTCTTACACTAGCACACATATCAAC
64 AGACATGGTCTTACACTAGCACACATATCAAC
*
4395656 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCCATGTCCCA
1 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG-CGATGCCATGTCCCA
* * ***
4395721 AATATGGTCTTATGTTAGCACACATATCAAC
65 GACATGGTCTTACACTAGCACACATATCAAC
4395752 CGAATGTCTT
Statistics
Matches: 247, Mismatches: 34, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
94 3 0.01
95 64 0.26
96 178 0.72
97 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (95 bp):
ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCACACATATCAAC
Found at i:4395731 original size:144 final size:144
Alignment explanation
Indices: 4395369--4395732 Score: 371
Period size: 144 Copynumber: 2.5 Consensus size: 144
4395359 AGGGTAAAAT
* * * *
4395369 ACCGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATAACAATACCGATGCCATGTTCC
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC-TCATAA-TATGCCGATGCCATGTCCC
* * * * *
4395433 AAGCATGATCTTACACTGGCCGCATATTGAGGCCGATGCCATATCCCAAACATGGTCTTACATTG
64 AAACATGGTCTTACACTGGCCGCATAATGAGGCCGATGCCATATCCCAAACATGGTCTTACACTA
* * ***
4395498 GCTCTCATAATGTGGC
129 GCACACATAATGCAAC
* * * *
4395514 A--GATGCCATGTCCCAGACATGGTCTTACACTAGCACACAT-ATCAAAGTCGATGCCATGTCCC
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAAT--ATGCCGATGCCATGTCCC
* * * * * * * *
4395576 AGACATAGTCTTACACTGGCTCTCATAATGTGGTCGATGCCATGTCTCAGACATGGTCTTACACT
64 AAACATGGTCTTACACTGGC-CGCATAATGAGGCCGATGCCATATCCCAAACATGGTCTTACACT
4395641 AGCACACAT-AT-CAAC
128 AGCACACATAATGCAAC
* *
4395656 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCCATGTCCCA
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATAT-GCCGATGCCATGTCCCA
*
4395721 AATATGGTCTTA
65 AACATGGTCTTA
4395733 TGTTAGCACA
Statistics
Matches: 176, Mismatches: 35, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
142 3 0.02
143 68 0.39
144 102 0.58
145 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (144 bp):
ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATATGCCGATGCCATGTCCCAA
ACATGGTCTTACACTGGCCGCATAATGAGGCCGATGCCATATCCCAAACATGGTCTTACACTAGC
ACACATAATGCAAC
Found at i:4399864 original size:16 final size:16
Alignment explanation
Indices: 4399843--4399873 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4399833 TTGTTTTTAA
*
4399843 TTTAAAATAATATTTT
1 TTTAAAAAAATATTTT
4399859 TTTAAAAAAATATTT
1 TTTAAAAAAATATTT
4399874 AGTTAAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAAAAAATATTTT
Found at i:4402332 original size:34 final size:34
Alignment explanation
Indices: 4402293--4402360 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
4402283 CAAACTTTAA
*
4402293 ATGCAATGGTTCTCCTTCAGAACTGTCACTAAGT
1 ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
4402327 ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
1 ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
4402361 CTACCATTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (34 bp):
ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
Done.