Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 21 of 27
Found at i:3112397 original size:16 final size:15
Alignment explanation
Indices: 3112376--3112406 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3112366 TTTTAGTTTG
3112376 TTGATTGAATTAAATT
1 TTGATTGAA-TAAATT
3112392 TTGATTGAATAAATT
1 TTGATTGAATAAATT
3112407 AATTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (15 bp):
TTGATTGAATAAATT
Found at i:3112691 original size:21 final size:20
Alignment explanation
Indices: 3112654--3112703 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
3112644 GAAAATTTGA
3112654 TTTAACTTTATATTTAACTT-G
1 TTTAA-TTTATATTTAA-TTGG
*
3112675 TTTAATTTATTTGTTAATTGG
1 TTTAATTTATAT-TTAATTGG
3112696 TTT-ATTTA
1 TTTAATTTA
3112704 GTTGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTAATTTATATTTAATTGG
Found at i:3115938 original size:12 final size:12
Alignment explanation
Indices: 3115923--3115947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3115913 AATTTAATTA
3115923 ATTTAATTTTTT
1 ATTTAATTTTTT
3115935 ATTTAATTTTTT
1 ATTTAATTTTTT
3115947 A
1 A
3115948 ACCATGTGTA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTAATTTTTT
Found at i:3116463 original size:14 final size:14
Alignment explanation
Indices: 3116441--3116483 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3116431 TAATTTATAT
3116441 ATATATATATATTA
1 ATATATATATATTA
*
3116455 ATATTTATATATTA
1 ATATATATATATTA
*
3116469 TTATA-ATATAATTA
1 ATATATATAT-ATTA
3116483 A
1 A
3116484 ATTTACATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATATATATTA
Found at i:3117236 original size:14 final size:14
Alignment explanation
Indices: 3117217--3117243 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3117207 CTCGATTCTA
3117217 ATTTTTCTTTTATC
1 ATTTTTCTTTTATC
3117231 ATTTTTCTTTTAT
1 ATTTTTCTTTTAT
3117244 TATCAAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTTCTTTTATC
Found at i:3117952 original size:9 final size:10
Alignment explanation
Indices: 3117937--3117961 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3117927 GACAGAACAA
3117937 AAAAAAAAGG
1 AAAAAAAAGG
3117947 AAAAAAAAGG
1 AAAAAAAAGG
3117957 AAAAA
1 AAAAA
3117962 GGAAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:3118126 original size:21 final size:22
Alignment explanation
Indices: 3118102--3118151 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
3118092 AGAAAATCGA
3118102 GAAAGAAAGA-G-AGGAAAAAAG
1 GAAAGAAAGATGAAGG-AAAAAG
*
3118123 GAAA-AAAAATGAAGGAAAAAG
1 GAAAGAAAGATGAAGGAAAAAG
3118144 G-AAGAAAG
1 GAAAGAAAG
3118152 GAAAAGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (22 bp):
GAAAGAAAGATGAAGGAAAAAG
Found at i:3118139 original size:14 final size:14
Alignment explanation
Indices: 3118120--3118175 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
3118110 GAGAGGAAAA
3118120 AAGGAAAAAAAATG
1 AAGGAAAAAAAATG
*
3118134 AAGGAAAAAGGAA-G
1 AAGGAAAAA-AAATG
* *
3118148 AAAGGAAAAGAGATG
1 -AAGGAAAAAAAATG
*
3118163 AAAGAAAAAAAAT
1 AAGGAAAAAAAAT
3118176 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (14 bp):
AAGGAAAAAAAATG
Found at i:3118146 original size:29 final size:29
Alignment explanation
Indices: 3118102--3118171 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
3118092 AGAAAATCGA
3118102 GAAAGAAAGAGAGGAAAAAAGGAAAAAAAAT
1 GAAAGAAA-A-AGGAAAAAAGGAAAAAAAAT
* * * *
3118133 GAAGGAAAAAGGAAGAAAGGAAAAGAGAT
1 GAAAGAAAAAGGAAAAAAGGAAAAAAAAT
3118162 GAAAGAAAAA
1 GAAAGAAAAA
3118172 AAATATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 26 0.76
30 1 0.03
31 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (29 bp):
GAAAGAAAAAGGAAAAAAGGAAAAAAAAT
Found at i:3118369 original size:32 final size:32
Alignment explanation
Indices: 3118286--3118369 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 32
3118276 GGAAAATGAA
*
3118286 GAAAAAAAAAAGAG-AAATAAAGAGAAGAAAG
1 GAAAAAAAAAAGGGAAAATAAAGAGAAGAAAG
* * **
3118317 GAAAGAAGTAAAAGGAAAAATAGTGGAGAAG-AAG
1 GAAA-AA-AAAAAGGGAAAATA-AAGAGAAGAAAG
3118351 GAAAAAAAAAAGGGAAAAT
1 GAAAAAAAAAAGGGAAAAT
3118370 TATGTAGTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
31 4 0.10
32 13 0.31
33 7 0.17
34 12 0.29
35 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (32 bp):
GAAAAAAAAAAGGGAAAATAAAGAGAAGAAAG
Found at i:3118874 original size:24 final size:24
Alignment explanation
Indices: 3118847--3118896 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3118837 TAAAGTGATT
3118847 AAGACTTATATTTGATTCACTCAA
1 AAGACTTATATTTGATTCACTCAA
3118871 AAGACTTATATTTGATTCACTCAA
1 AAGACTTATATTTGATTCACTCAA
3118895 AA
1 AA
3118897 AAATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (24 bp):
AAGACTTATATTTGATTCACTCAA
Found at i:3118910 original size:26 final size:24
Alignment explanation
Indices: 3118850--3118907 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
3118840 AGTGATTAAG
*
3118850 ACTTATATTTGATTCACTCAAAAG
1 ACTTATATTTGATTCACTCAAAAA
3118874 ACTTATATTTGATTCACTCAAAAA
1 ACTTATATTTGATTCACTCAAAAA
* *
3118898 AATTTTATTT
1 ACTTATATTT
3118908 TTGTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (24 bp):
ACTTATATTTGATTCACTCAAAAA
Found at i:3120710 original size:18 final size:18
Alignment explanation
Indices: 3120687--3120723 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3120677 AAATAAAAAA
3120687 TACATATTTACTTTCCTT
1 TACATATTTACTTTCCTT
3120705 TACATATTTACTTTCCTT
1 TACATATTTACTTTCCTT
3120723 T
1 T
3120724 CCCTAACCTC
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:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (18 bp):
TACATATTTACTTTCCTT
Found at i:3122398 original size:22 final size:22
Alignment explanation
Indices: 3122355--3122398 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3122345 TAAATTTACA
* *
3122355 TCTTAATATTTATAATTTATTT
1 TCTTAATATTTATAAATGATTT
3122377 TCTT-ATATTTATATAATGATTT
1 TCTTAATATTTATA-AATGATTT
3122399 CTTTTATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (22 bp):
TCTTAATATTTATAAATGATTT
Found at i:3124730 original size:30 final size:29
Alignment explanation
Indices: 3124663--3124731 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
3124653 TTTTGAATTT
* *
3124663 TTATCTTTTTAAGATCTAAATTTTTTTCA
1 TTATCTTTTTAAGATCTAAAATTTTTTAA
* * * *
3124692 TAAACTTTTTACGAGTTTAAAATTTTTTAA
1 TTATCTTTTTAAGA-TCTAAAATTTTTTAA
3124722 TTATCTTTTT
1 TTATCTTTTT
3124732 TTTTACATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.58
Consensus pattern (29 bp):
TTATCTTTTTAAGATCTAAAATTTTTTAA
Found at i:3125253 original size:27 final size:27
Alignment explanation
Indices: 3125223--3125284 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 27
3125213 TTCTTATGGC
3125223 ATTTTAAATAGAA-TTTT-ATATGATTAA
1 ATTTTAAATA-AATTTTTCATATG-TTAA
*
3125250 ATTTTTAATTAAATTTTTTCATATGTTAA
1 A-TTTTAAATAAA-TTTTTCATATGTTAA
3125279 ATTTTA
1 ATTTTA
3125285 GTTAAGGCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 3 0.10
28 13 0.43
29 9 0.30
30 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (27 bp):
ATTTTAAATAAATTTTTCATATGTTAA
Found at i:3125256 original size:28 final size:28
Alignment explanation
Indices: 3125224--3125283 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
3125214 TCTTATGGCA
3125224 TTTTAAATAGAA-TTTT-ATATGATTAAAT
1 TTTTAAATA-AATTTTTCATATG-TTAAAT
*
3125252 TTTTAATTAAATTTTTTCATATGTTAAAT
1 TTTTAAATAAA-TTTTTCATATGTTAAAT
3125281 TTT
1 TTT
3125284 AGTTAAGGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.07
28 8 0.29
29 13 0.46
30 5 0.18
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTTAAATAAATTTTTCATATGTTAAAT
Found at i:3127600 original size:157 final size:157
Alignment explanation
Indices: 3127267--3127601 Score: 413
Period size: 157 Copynumber: 2.1 Consensus size: 157
3127257 CCTTGGGATA
* * * * * ***
3127267 TTTTGTAATTTTACTTTATAATTGAGTCTTTTAGGATCAACATGATACTTTTATGTTGAAGGTGT
1 TTTTGTAATTTTACTTTAGAATCGAATCCTTTAGGATCAACATGATACTTTCATGCCAAAGGTGT
* * * *
3127332 GCTTTAAGGATATGTTCTTCATTTCGTATCATTATTGAGTCTTTTAGAATTACCGAGATACTATC
66 GCTTTAAGAATATGTTCATCATTTCATATCATTATTGAGTCCTTTAGAATTACCGAGATACTATC
* * *
3127397 ATGTTAAAAGTATATTTTAGAGGACAT
131 ATGTTAAAAGTATAATTTAAAAGACAT
* * * *
3127424 TTTAGTAATTTTACCTTAGAATCGAATCCTTTAGGATCACCGA-GGTACTTTCATGCCAAAGGTG
1 TTTTGTAATTTTACTTTAGAATCGAATCCTTTAGGATCAAC-ATGATACTTTCATGCCAAAGGTG
* ** *
3127488 TGCTTTACA-AATATGTTCATCATTTTATATCATTATTGAGTCCTTTAGGTTTACCGAGATACTT
65 TGCTTTA-AGAATATGTTCATCATTTCATATCATTATTGAGTCCTTTAGAATTACCGAGATACTA
*
3127552 TCATGTTGAAAGTATAATTTAAAAGACAT
129 TCATGTTAAAAGTATAATTTAAAAGACAT
*
3127581 TTTTGTAATTTTATTTTAGAA
1 TTTTGTAATTTTACTTTAGAA
3127602 CCAAGATCAT
Statistics
Matches: 149, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
157 147 0.99
158 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.43
Consensus pattern (157 bp):
TTTTGTAATTTTACTTTAGAATCGAATCCTTTAGGATCAACATGATACTTTCATGCCAAAGGTGT
GCTTTAAGAATATGTTCATCATTTCATATCATTATTGAGTCCTTTAGAATTACCGAGATACTATC
ATGTTAAAAGTATAATTTAAAAGACAT
Found at i:3127643 original size:157 final size:156
Alignment explanation
Indices: 3127297--3127643 Score: 360
Period size: 157 Copynumber: 2.2 Consensus size: 156
3127287 ATTGAGTCTT
* * * *
3127297 TTAGGATCAAC-ATGATACTTTTATGTTGAAGGTGTGCTTTAAGGATATGTTCTTCATTTCGTAT
1 TTAGGATCAACGA-AATACTTTTAT-TTGAAGGTGTGCTTTAAGAATATGTTCATCATTTCATAT
* * * *
3127361 CATTATTGAGTCTTTTAGAATTACCGAGATACTATCATGTTAAAAGTATATTTTAGAGGACATTT
64 CATTATTGAGTCCTTTAGAATTACCGAGATACTATCATGTTAAAAGTATAATTTAAAAGACATTT
* * *
3127426 TAGTAATTTTACCTTAGAATCGAATCCT
129 TAGTAATTTTACCTTAGAACCAAATCCA
* ** * *** *
3127454 TTAGGATCACCGAGGTACTTTCATGCCAAAGGTGTGCTTTACA-AATATGTTCATCATTTTATAT
1 TTAGGATCAACGAAATACTTTTAT-TTGAAGGTGTGCTTTA-AGAATATGTTCATCATTTCATAT
** * *
3127518 CATTATTGAGTCCTTTAGGTTTACCGAGATACTTTCATGTTGAAAGTATAATTTAAAAGACATTT
64 CATTATTGAGTCCTTTAGAATTACCGAGATACTATCATGTTAAAAGTATAATTTAAAAGACATTT
* **
3127583 TTGTAATTTTATTTTAGAACCAAGAT-CA
129 TAGTAATTTTACCTTAGAACCAA-ATCCA
*
3127611 TTA-GAGTTAACGAAATACTTTTATTTGGAAGGT
1 TTAGGA-TCAACGAAATACTTTTATTT-GAAGGT
3127644 ACACTTTTGG
Statistics
Matches: 153, Mismatches: 32, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
156 2 0.01
157 147 0.96
158 4 0.03
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (156 bp):
TTAGGATCAACGAAATACTTTTATTTGAAGGTGTGCTTTAAGAATATGTTCATCATTTCATATCA
TTATTGAGTCCTTTAGAATTACCGAGATACTATCATGTTAAAAGTATAATTTAAAAGACATTTTA
GTAATTTTACCTTAGAACCAAATCCA
Found at i:3130960 original size:20 final size:18
Alignment explanation
Indices: 3130913--3130987 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 18
3130903 AAAAAGACAT
3130913 AATGTATCGATACATTATA
1 AATGTATCGATACATTA-A
*
3130932 GAATATATCGATACATTCAA
1 -AATGTATCGATACATT-AA
*
3130952 ACATGTATCGATATATTGAAA
1 A-ATGTATCGATACATT--AA
3130973 AATGTATCGATACAT
1 AATGTATCGATACAT
3130988 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 1 0.02
20 42 0.89
21 4 0.09
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (18 bp):
AATGTATCGATACATTAA
Found at i:3131668 original size:29 final size:29
Alignment explanation
Indices: 3131594--3132835 Score: 1353
Period size: 28 Copynumber: 43.5 Consensus size: 29
3131584 CACCGACACG
* ** *
3131594 TGTGGGCTTTGAAAAGAGTTACTTCTGGCT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT
* *
3131624 TGTGGGCTTTGCAAAGAGTGTCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3131653 TATGGGCTTTGAAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3131681 TGTGGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3131709 TGTGGGCTTTGAAAA-AGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3131737 TATGGGC-TTGAAAA-AGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
3131764 TGTGGGCTTTGAAAA-AGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3131792 TGTGGGC-TTGAAAA-AGTTCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
3131819 TGTGGGC-TTGAAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
** *
3131846 AATGGGCTTTGAAATG-GTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
**
3131874 CATGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
** * *
3131903 CATGGGCTTTGAAAGGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3131932 TGCGTGGGCTTTGAAAAGAGTGCTAATGACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACT
3131963 TGCGTGGGCTTT-AAAAG-GTTGCCACTGACT
1 T--GTGGGCTTTGAAAAGAG-TGCCACTGACT
* *
3131993 TGCGTGGGCTTTGAAAGGA-TGCCACTAACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACT
*
3132023 TGTGGGCTTTG-AAAGAGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
** * *
3132051 CATGGGC-TTGAAAA-TGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132078 TGCGTGGACTTT-AAAAGGGTGCCACTGACTT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGAC-T
*
3132109 GTGTGGGCTTTGAAAGGA-TGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTGCCACTGACT
3132138 TGTGGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3132166 CGTGGGCTTTGAAAA-ATGTGCCACTGACT
1 TGTGGGCTTTGAAAAGA-GTGCCACTGACT
*
3132195 CGTGGGCTTTGAAAA-AGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132223 TGCGTGAGCTTT-AAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132253 TGCGTTGGCTTTGAAAGGA-TGCCACTGACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACT
*
3132283 TGTGGGCTTT-AAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132311 CGTGGGCTTTGAAAAG-GTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132339 CGTGGGC-TTG-AAAGGGTGCCACTGA-T
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3132365 TCGTGGGC-TTG--AAGGGTGCCACTGACT
1 T-GTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
3132392 TGTGGGTTTTGAACAGAGTACCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132421 TGTGGGCTTTGAAAGGAGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT
* *
3132451 TGTGTGGACTTTGAAAGGAGTGCCACTAACTT
1 TGTG-GG-CTTTGAAAAGAGTGCCACTGAC-T
*
3132483 GTGTGGGCTTTGAAAGGA-TGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3132512 TGTGGGCTTTG-AAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3132540 TGTGGGCTTCGAAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132568 TGTGGGCTTCG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
3132596 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
3132624 TGTGGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132652 TGTGGGC-TTGAAAA-TGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
3132679 TGTGGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132707 TGTGGGCTTTG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
3132735 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132764 TGTGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
3132793 CGTGGGCTTTGAAAAGAGTGTCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* **
3132822 CGTATGCTTTGAAA
1 TGTGGGCTTTGAAA
3132836 GGGATGAACA
Statistics
Matches: 1063, Mismatches: 102, Indels: 95
0.84 0.08 0.08
Matches are distributed among these distances:
26 24 0.02
27 157 0.15
28 424 0.40
29 221 0.21
30 148 0.14
31 69 0.06
32 16 0.02
33 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:3134105 original size:22 final size:22
Alignment explanation
Indices: 3134046--3134105 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3134036 CATCTAGACC
* *
3134046 CTTTTCTTTTTTTTGCTATTTTT
1 CTTTTGTTTTTTTT-TTATTTTT
*
3134069 -TCTTGGTTTTTTTTTTATTTTT
1 CT-TTTGTTTTTTTTTTATTTTT
3134091 CTTTTGTTTTTTTTT
1 CTTTTGTTTTTTTTT
3134106 GGGTGTAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.03, C:0.08, G:0.07, T:0.82
Consensus pattern (22 bp):
CTTTTGTTTTTTTTTTATTTTT
Found at i:3141884 original size:20 final size:20
Alignment explanation
Indices: 3141856--3141930 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3141846 TCATACCCTG
3141856 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3141876 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3141896 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
3141916 ATGTATCGATACATT
1 ATGTATCGATACATT
3141931 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3141923 original size:40 final size:39
Alignment explanation
Indices: 3141856--3141933 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3141846 TCATACCCTG
* *
3141856 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
3141896 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
3141934 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:3149052 original size:22 final size:23
Alignment explanation
Indices: 3149023--3149074 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3149013 AATGAAAAGA
* *
3149023 AAAAAAAAGTGCAA-AAGCAAAAT
1 AAAAAAAAGAG-AACAAGAAAAAT
3149046 AAAAAAAAGAGAACAAGAAAAAT
1 AAAAAAAAGAGAACAAGAAAAAT
3149069 AAAAAA
1 AAAAAA
3149075 CGAGGACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.77, C:0.06, G:0.12, T:0.06
Consensus pattern (23 bp):
AAAAAAAAGAGAACAAGAAAAAT
Found at i:3149053 original size:40 final size:40
Alignment explanation
Indices: 3148985--3149072 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
3148975 TCAAAATGAC
* *
3148985 AAAAAAAGTCAAAAGCAAAAGCACAAAAAA-TGAA-AAGAA
1 AAAAAAAGTCAAAAGCAAAAG-AAAAAAAAGAGAACAAGAA
*
3149024 AAAAAAAGTGCAAAAGCAAAATAAAAAAAAGAGAACAAGAA
1 AAAAAAAGT-CAAAAGCAAAAGAAAAAAAAGAGAACAAGAA
3149065 AAATAAAA
1 AAA-AAAA
3149073 AACGAGGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 16 0.38
40 14 0.33
41 8 0.19
42 4 0.10
ACGTcount: A:0.74, C:0.08, G:0.12, T:0.06
Consensus pattern (40 bp):
AAAAAAAGTCAAAAGCAAAAGAAAAAAAAGAGAACAAGAA
Found at i:3149339 original size:12 final size:11
Alignment explanation
Indices: 3149319--3149352 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
3149309 CCAATCCTAA
3149319 AAAAAAAAAAC
1 AAAAAAAAAAC
3149330 AAAAACAAAAAC
1 AAAAA-AAAAAC
3149342 AAAAAAAAAAC
1 AAAAAAAAAAC
3149353 CCTTTTCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:3150439 original size:27 final size:27
Alignment explanation
Indices: 3150402--3151277 Score: 1455
Period size: 27 Copynumber: 32.0 Consensus size: 27
3150392 GTGGCATTTT
* * *
3150402 CTTTTAAAGTCCACAATTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
3150430 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150457 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
3150485 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150512 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150539 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150566 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
*
3150594 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
3150622 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150649 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3150676 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150703 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
3150731 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
3150759 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
3150787 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150814 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3150841 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150868 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
3150896 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3150923 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3150950 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3150977 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
3151004 CTTTTAAGTCCACAACTCTGTGGCGCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3151031 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
3151059 CTTTTCAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
3151087 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3151114 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3151141 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3151168 CTTTTAAAGTCTACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
3151196 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
3151223 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
3151250 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
3151277 C
1 C
3151278 ATTTCAAAGC
Statistics
Matches: 806, Mismatches: 35, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
27 538 0.67
28 268 0.33
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:3150509 original size:82 final size:81
Alignment explanation
Indices: 3150402--3151277 Score: 1464
Period size: 82 Copynumber: 10.7 Consensus size: 81
3150392 GTGGCATTTT
* * * *
3150402 CTTTTAAAGTCCACAATTCTGTGGCATCTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT-AAGT
3150467 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* *
3150485 CTTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
3150550 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
*
3150566 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTTAGT
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGT
3150631 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
3150649 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
3150714 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* *
3150731 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGA
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCTGTGGCA-CCCTTTTAAGT
3150796 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
3150814 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT-AAGTC
3150879 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
3150896 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
3150961 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* *
3150977 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCGCCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
3151042 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* * *
3151059 CTTTTCAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTC
3151124 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * *
3151141 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCTACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGTC
3151206 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
3151223 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCC
3151278 ATTTCAAAGC
Statistics
Matches: 750, Mismatches: 34, Indels: 20
0.93 0.04 0.02
Matches are distributed among these distances:
81 200 0.27
82 367 0.49
83 157 0.21
84 26 0.03
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:3151315 original size:32 final size:32
Alignment explanation
Indices: 3151260--3151829 Score: 980
Period size: 32 Copynumber: 17.8 Consensus size: 32
3151250 CTTTTAAATC
* *
3151260 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151291 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151323 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151355 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151387 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3151419 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151451 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151483 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3151515 CACAAGTCGGTGGTAACCCATGTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3151547 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3151579 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151611 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3151643 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3151675 CACAAGTCGGTGGTAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3151707 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3151739 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3151771 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * * *
3151803 TGCAAGTCTGTGGCAACTCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
3151830 TCACCATTTT
Statistics
Matches: 515, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
31 12 0.02
32 503 0.98
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:3152385 original size:20 final size:20
Alignment explanation
Indices: 3152357--3152431 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3152347 TCATACCCTG
3152357 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3152377 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3152397 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
3152417 ATGTATCGATACATT
1 ATGTATCGATACATT
3152432 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3152424 original size:40 final size:39
Alignment explanation
Indices: 3152357--3152434 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3152347 TCATACCCTG
* *
3152357 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
3152397 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
3152435 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:3162250 original size:19 final size:19
Alignment explanation
Indices: 3162226--3162265 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3162216 AAATAATGGG
*
3162226 AATGAATAGCAAGAAAAAA
1 AATGAACAGCAAGAAAAAA
* *
3162245 AATGAACATCAATAAAAAA
1 AATGAACAGCAAGAAAAAA
3162264 AA
1 AA
3162266 AGTGGTCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.12
Consensus pattern (19 bp):
AATGAACAGCAAGAAAAAA
Found at i:3166557 original size:20 final size:18
Alignment explanation
Indices: 3166510--3166584 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 18
3166500 AAAAAGACAT
3166510 AATGTATCGATACATTATA
1 AATGTATCGATACATTA-A
*
3166529 GAATATATCGATACATTCAA
1 -AATGTATCGATACATT-AA
*
3166549 ACATGTATCGATATATTGAAA
1 A-ATGTATCGATACATT--AA
3166570 AATGTATCGATACAT
1 AATGTATCGATACAT
3166585 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 1 0.02
20 42 0.89
21 4 0.09
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (18 bp):
AATGTATCGATACATTAA
Found at i:3168157 original size:3 final size:3
Alignment explanation
Indices: 3168149--3168189 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3168139 CACTACAAAC
3168149 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3168190 GGACTAGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3168392 original size:40 final size:39
Alignment explanation
Indices: 3168290--3168414 Score: 169
Period size: 39 Copynumber: 3.2 Consensus size: 39
3168280 TTTGAGTTTA
* * * * *
3168290 TTTGAGTAAAAACTAAGTTTTTAAGGTCATGTTAGTAAT
1 TTTGAGTAAAAATTTAGCTTTTAGGGTCATTTTAGTAAT
*
3168329 TTTGAGTTAAAATTTAGCTTTTAGGGTCATTTTAGTAAT
1 TTTGAGTAAAAATTTAGCTTTTAGGGTCATTTTAGTAAT
* *
3168368 TTAGAGTAAAAAATTTAGCTTTTAGGGTTATTTTAGTAAT
1 TTTGAGT-AAAAATTTAGCTTTTAGGGTCATTTTAGTAAT
3168408 TTTGAGT
1 TTTGAGT
3168415 TAAAGTTTGG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 39 0.52
40 36 0.48
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (39 bp):
TTTGAGTAAAAATTTAGCTTTTAGGGTCATTTTAGTAAT
Found at i:3168441 original size:40 final size:39
Alignment explanation
Indices: 3168290--3168451 Score: 162
Period size: 40 Copynumber: 4.1 Consensus size: 39
3168280 TTTGAGTTTA
* * * * *
3168290 TTTGAGTAAAAACTAAGTTTTTAAGGTCATGTTAGTAAT
1 TTTGAGTTAAAATTTAGCTTTTAAGGTCATTTTAGTAAT
*
3168329 TTTGAGTTAAAATTTAGCTTTTAGGGTCATTTTAGTAAT
1 TTTGAGTTAAAATTTAGCTTTTAAGGTCATTTTAGTAAT
* * * *
3168368 TTAGAGTAAAAAATTTAGCTTTTAGGGTTATTTTAGTAAT
1 TTTGAGT-TAAAATTTAGCTTTTAAGGTCATTTTAGTAAT
* * * * * *
3168408 TTTGAGTTAAAGTTTGGTTTTTAAAAGTCATTTTAATAAA
1 TTTGAGTTAAAATTTAGCTTTT-AAGGTCATTTTAGTAAT
3168448 TTTG
1 TTTG
3168452 TGCTAAAACT
Statistics
Matches: 102, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
39 50 0.49
40 52 0.51
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (39 bp):
TTTGAGTTAAAATTTAGCTTTTAAGGTCATTTTAGTAAT
Found at i:3175714 original size:31 final size:32
Alignment explanation
Indices: 3175672--3175731 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
3175662 TATCATATTT
3175672 ATATTAATTTAT-TATTAT-AATTATATTTAAA
1 ATATTAATTTATATATTATAAATTA-ATTTAAA
* *
3175703 ATATTATTTTATATTTTATAAATTAATTT
1 ATATTAATTTATATATTATAAATTAATTT
3175732 TGATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.44
32 9 0.36
33 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATATTAATTTATATATTATAAATTAATTTAAA
Found at i:3175727 original size:19 final size:21
Alignment explanation
Indices: 3175692--3175748 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
3175682 ATTATTATAA
*
3175692 TTATA-TTTAAAATATT-ATT
1 TTATATTTTATAATATTAATT
3175711 TTATATTTTATAA-ATTAATT
1 TTATATTTTATAATATTAATT
3175731 TTGATATATTTAT-ATATT
1 TT-ATAT-TTTATAATATT
3175749 TATATCGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.25
20 11 0.34
21 5 0.16
22 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATATTTTATAATATTAATT
Found at i:3175786 original size:25 final size:23
Alignment explanation
Indices: 3175756--3175812 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
3175746 ATTTATATCG
3175756 TATTTATATAATTTTTTAAATTAA
1 TATTTATATAATTTTTTAAATT-A
* *
3175780 TATTT-TAATTATTTTTTTATATTA
1 TATTTAT-A-TAATTTTTTAAATTA
3175804 TATTTATAT
1 TATTTATAT
3175813 CTCATAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTTATATAATTTTTTAAATTA
Found at i:3177928 original size:12 final size:12
Alignment explanation
Indices: 3177911--3177935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3177901 TTTATTATAT
3177911 TATATATATAAA
1 TATATATATAAA
3177923 TATATATATAAA
1 TATATATATAAA
3177935 T
1 T
3177936 GTTGGAGTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATATATAAA
Found at i:3178609 original size:2 final size:2
Alignment explanation
Indices: 3178602--3178637 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3178592 CTATGTTGCA
*
3178602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3178638 TTATTATGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3183260 original size:21 final size:21
Alignment explanation
Indices: 3183223--3183265 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3183213 ACATTTTTTA
*
3183223 ATATTTATATTACTATATTAT
1 ATATTTATATTACTATAATAT
*
3183244 ATATTTATTTTTA-TATAATAT
1 ATATTTA-TATTACTATAATAT
3183265 A
1 A
3183266 AATTACGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTTATATTACTATAATAT
Found at i:3184028 original size:3 final size:3
Alignment explanation
Indices: 3184020--3184064 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3184010 GAAAAACATA
3184020 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3184065 GGGTTGGACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3187414 original size:20 final size:19
Alignment explanation
Indices: 3187386--3187459 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
3187376 TTTTAACTAG
3187386 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAA-A
* *
3187406 ATATATCGATACATTCAAA
1 ATGTATCGATACATTGAAA
*
3187425 CATGTATCGATATATTGAAAA
1 -ATGTATCGATACATTG-AAA
*
3187446 ATGTATCAATACAT
1 ATGTATCGATACAT
3187460 CTAGGTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.91
21 3 0.07
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACATTGAAA
Found at i:3187946 original size:45 final size:45
Alignment explanation
Indices: 3187877--3188043 Score: 185
Period size: 45 Copynumber: 3.6 Consensus size: 45
3187867 AACTAAGAGA
* *
3187877 AAAGTGGACCAATGTGCTGATTCAAGACCAGCGACATTAGGCTAAT
1 AAAGTGGA-CAATGTGCTGATTCAAGGCCAGCAACATTAGGCTAAT
* *
3187923 AAAGTTGACAATGTGCTGATTCAAGGCCAGCAACATT-GAGCTAAGAG
1 AAAGTGGACAATGTGCTGATTCAAGGCCAGCAACATTAG-GCT-A-AT
* * *
3187970 AAAATGGATAATGTGCTGATTCAAGGCCAGCAACATTAAGCTAAT
1 AAAGTGGACAATGTGCTGATTCAAGGCCAGCAACATTAGGCTAAT
* * *
3188015 AAAG-GTGCCAATATGCTGATTCAATGCCA
1 AAAGTG-GACAATGTGCTGATTCAAGGCCA
3188044 ACGATATCGG
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
44 2 0.02
45 53 0.52
46 9 0.09
47 38 0.37
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (45 bp):
AAAGTGGACAATGTGCTGATTCAAGGCCAGCAACATTAGGCTAAT
Found at i:3187993 original size:47 final size:47
Alignment explanation
Indices: 3187837--3188013 Score: 198
Period size: 47 Copynumber: 3.8 Consensus size: 47
3187827 AGAGGATTGC
** * * *
3187837 CAATGTGCCAATTCAAGGCTAGCGACATTGAACTAAGAGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCAACATTGAGCTAAGAGAAAA-TGGA
* * * * *
3187885 CCAATGTGCTGATTCAAGACCAGCGACATT-AGGCT-A-ATAAAGTTGA
1 -CAATGTGCTGATTCAAGGCCAGCAACATTGA-GCTAAGAGAAAATGGA
3187931 CAATGTGCTGATTCAAGGCCAGCAACATTGAGCTAAGAGAAAATGGA
1 CAATGTGCTGATTCAAGGCCAGCAACATTGAGCTAAGAGAAAATGGA
* *
3187978 TAATGTGCTGATTCAAGGCCAGCAACATTAAGCTAA
1 CAATGTGCTGATTCAAGGCCAGCAACATTGAGCTAA
3188014 TAAAGGTGCC
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
45 30 0.28
46 5 0.05
47 45 0.41
48 2 0.02
49 27 0.25
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (47 bp):
CAATGTGCTGATTCAAGGCCAGCAACATTGAGCTAAGAGAAAATGGA
Found at i:3188016 original size:92 final size:94
Alignment explanation
Indices: 3187837--3188043 Score: 283
Period size: 92 Copynumber: 2.2 Consensus size: 94
3187827 AGAGGATTGC
** * *
3187837 CAATGTGCCAATTCAAGGCTAGCGACATTGAACTAAGAGAAAAGTGGACCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCAACATTGAACTAAGAGAAAAGTGGACCAATGTGCTGATTCAA
* * *
3187902 GACCAGCGACATTAGGCTAATAAAGTTGA
66 GACCAGCAACATTAAGCTAATAAAGGTGA
* *
3187931 CAATGTGCTGATTCAAGGCCAGCAACATTGAGCTAAGAGAAAA-TGGA-TAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCAACATTGAACTAAGAGAAAAGTGGACCAATGTGCTGATTCAA
* *
3187994 GGCCAGCAACATTAAGCTAATAAAGGTGC
66 GACCAGCAACATTAAGCTAATAAAGGTGA
* *
3188023 CAATATGCTGATTCAATGCCA
1 CAATGTGCTGATTCAAGGCCA
3188044 ACGATATCGG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 58 0.58
93 4 0.04
94 38 0.38
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (94 bp):
CAATGTGCTGATTCAAGGCCAGCAACATTGAACTAAGAGAAAAGTGGACCAATGTGCTGATTCAA
GACCAGCAACATTAAGCTAATAAAGGTGA
Found at i:3188181 original size:28 final size:29
Alignment explanation
Indices: 3188145--3188466 Score: 279
Period size: 28 Copynumber: 11.4 Consensus size: 29
3188135 ACTAACTTTC
*
3188145 TGTGGGCTTT-AAAGAGATGTCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
*
3188173 TGTGTGCTTTGAAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
*
3188201 TGTGGGCTTTGGAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* * *
3188229 CGTGGACTTTGAAA-AGTTGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* * *
3188257 CGTGAGCTTTGAAA-AGTTGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* * * *
3188285 TATGGGCTTGGAAA-AGATACCATTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
**
3188313 TGTGGGCTTTGAAA-AGATGCCACCAACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* *
3188341 TGTGGACATTGAAAG-GATGCCACTGACT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* *
3188369 TGTGGGCTTTGAAAG-GATGCCACGGAGT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* * * * *
3188397 TGTAGAC-TT-AAAAAGATGCCACGGAGT
1 TGTGGGCTTTGAAAGAGATGCCACTGACT
* * * * *
3188424 TATGGACTTTAAAAAGAAATGCCACTGAAT
1 TGTGGGCTTT-GAAAGAGATGCCACTGACT
* *
3188454 CGTGGACTTTGAA
1 TGTGGGCTTTGAA
3188467 GAGGTCACAG
Statistics
Matches: 244, Mismatches: 43, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
26 3 0.01
27 20 0.08
28 193 0.79
29 6 0.02
30 22 0.09
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTGAAAGAGATGCCACTGACT
Found at i:3188225 original size:56 final size:56
Alignment explanation
Indices: 3188145--3188466 Score: 308
Period size: 56 Copynumber: 5.7 Consensus size: 56
3188135 ACTAACTTTC
* *
3188145 TGTGGGCTTT-AAAGAGATGTCACTGACTTGTGTG-CTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACTTGTG-GACTTTGAAAAGATGCCACTGACT
* * *
3188201 TGTGGGCTTTGGAAGGATGCCACTGACTCGTGGACTTTGAAAAGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGACT
* * * * * * * * *
3188257 CGTGAGCTTTGAAAAGTTGCCACTGACTTATGGGCTTGGAAAAGATACCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGACT
* ** * *
3188313 TGTGGGCTTTGAAAAGATGCCACCAACTTGTGGACATTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGACT
* * * * * *
3188369 TGTGGGCTTTGAAAGGATGCCACGGAGTTGTAGAC-TTAAAAAGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGACT
* * * * * *
3188424 TATGGACTTTAAAAAGAAATGCCACTGAATCGTGGACTTTGAA
1 TGTGGGCTTT-GAAAG-GATGCCACTGACTTGTGGACTTTGAA
3188467 GAGGTCACAG
Statistics
Matches: 214, Mismatches: 47, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
55 25 0.12
56 167 0.78
57 18 0.08
58 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGATGCCACTGACT
Found at i:3188419 original size:27 final size:28
Alignment explanation
Indices: 3188375--3188440 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
3188365 GACTTGTGGG
* * *
3188375 CTTTGAAAGGATGCCACGGAGTTGTAGA
1 CTTTAAAAAGATGCCACGGAGTTATAGA
*
3188403 C-TTAAAAAGATGCCACGGAGTTATGGA
1 CTTTAAAAAGATGCCACGGAGTTATAGA
3188430 CTTTAAAAAGA
1 CTTTAAAAAGA
3188441 AATGCCACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (28 bp):
CTTTAAAAAGATGCCACGGAGTTATAGA
Found at i:3195618 original size:27 final size:30
Alignment explanation
Indices: 3195577--3195654 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 30
3195567 TTAATTTAGC
3195577 TTCTTGTAATTTTTAATTTATGCAA-T-TT
1 TTCTTGTAATTTTTAATTTATGCAATTATT
* *
3195605 TT-TTGTATTTTTTAATTTATGTAATTTATT
1 TTCTTGTAATTTTTAATTTATGCAA-TTATT
3195635 TTCTTGTAATTTTTAATTTA
1 TTCTTGTAATTTTTAATTTA
3195655 CATAATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 20 0.47
28 2 0.05
29 1 0.02
30 4 0.09
31 16 0.37
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.65
Consensus pattern (30 bp):
TTCTTGTAATTTTTAATTTATGCAATTATT
Found at i:3195642 original size:31 final size:31
Alignment explanation
Indices: 3195568--3195670 Score: 124
Period size: 31 Copynumber: 3.5 Consensus size: 31
3195558 GTCATGTAGT
**
3195568 TAATTTAGCTTCTTGTAATTTTTAATTTATG
1 TAATTTATTTTCTTGTAATTTTTAATTTATG
* *
3195599 CAA--T-TTTT-TTGTATTTTTTAATTTATG
1 TAATTTATTTTCTTGTAATTTTTAATTTATG
**
3195626 TAATTTATTTTCTTGTAATTTTTAATTTACA
1 TAATTTATTTTCTTGTAATTTTTAATTTATG
3195657 TAATTTATTTTCTT
1 TAATTTATTTTCTT
3195671 ACAATTTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
27 20 0.33
28 2 0.03
29 2 0.03
30 4 0.07
31 32 0.53
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (31 bp):
TAATTTATTTTCTTGTAATTTTTAATTTATG
Found at i:3195677 original size:31 final size:31
Alignment explanation
Indices: 3195613--3195677 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
3195603 TTTTTTGTAT
** **
3195613 TTTTTAATTTATGTAATTTATTTTCTTGTAA
1 TTTTTAATTTACATAATTTATTTTCTTACAA
3195644 TTTTTAATTTACATAATTTATTTTCTTACAA
1 TTTTTAATTTACATAATTTATTTTCTTACAA
3195675 TTT
1 TTT
3195678 AAATTTTCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTTTAATTTACATAATTTATTTTCTTACAA
Found at i:3195719 original size:14 final size:15
Alignment explanation
Indices: 3195694--3195722 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3195684 TCACAATCCT
3195694 TGCAATTTAAATTTA
1 TGCAATTTAAATTTA
3195709 TGCAA-TTAAATTTA
1 TGCAATTTAAATTTA
3195723 AATTTATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (15 bp):
TGCAATTTAAATTTA
Found at i:3199025 original size:25 final size:25
Alignment explanation
Indices: 3198974--3199027 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
3198964 ATTTACGAAT
* *
3198974 TAATTATTAAAATTATATTTATAAA
1 TAATGATTAAAATTATATTAATAAA
3198999 TAATGATTAAAATTATATTAA-ATAA
1 TAATGATTAAAATTATATTAATA-AA
3199024 TAAT
1 TAAT
3199028 AAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATGATTAAAATTATATTAATAAA
Found at i:3206281 original size:98 final size:98
Alignment explanation
Indices: 3206160--3206345 Score: 291
Period size: 98 Copynumber: 1.9 Consensus size: 98
3206150 TTTTCTTAAA
* * ** *
3206160 AAATTAATTTGTTACGTATGCAATTGTAACATATAGAATTTAGATCACATGTTGAAGAATAAATG
1 AAATTAATTTGTTACATACGCAATTAAAACATATAAAATTTAGATCACATGTTGAAGAATAAATG
3206225 ATTTTCTTATAAATTTACATGGACATAAAGTTT
66 ATTTTCTTATAAATTTACATGGACATAAAGTTT
* * *
3206258 AAATTAATTTGTTACATGCGCAATTAAAAGATATAAAATTTAGATCATATGTTGAAGAATAAATG
1 AAATTAATTTGTTACATACGCAATTAAAACATATAAAATTTAGATCACATGTTGAAGAATAAATG
*
3206323 ATTTTCTTATAAATTTATATGGA
66 ATTTTCTTATAAATTTACATGGA
3206346 TTAAAATTCT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (98 bp):
AAATTAATTTGTTACATACGCAATTAAAACATATAAAATTTAGATCACATGTTGAAGAATAAATG
ATTTTCTTATAAATTTACATGGACATAAAGTTT
Found at i:3207370 original size:67 final size:67
Alignment explanation
Indices: 3207263--3207441 Score: 213
Period size: 67 Copynumber: 2.7 Consensus size: 67
3207253 TAAACGACCA
* * * * *
3207263 AGACAAACTGATAA-AAGCTGAAATAGAAGATCATAATGGGGAATTTGC-GGTTCTTATCAACAG
1 AGACAAACTGATAATAGGCTGAAATAAAAGATCATAATGGGGAATATGCAGCTTC-CATCAACAG
*
3207326 TTG
65 CTG
*
3207329 AGACAAACTGATAATAGGCTGAAATAAAAGATCATAATGGGGAATATGCAGCTTCCATCAATAGC
1 AGACAAACTGATAATAGGCTGAAATAAAAGATCATAATGGGGAATATGCAGCTTCCATCAACAGC
3207394 TG
66 TG
* * *
3207396 AGACAAACTGATAAT-GAGCT-AGAATAAAAGATTATGATGGGAAATA
1 AGACAAACTGATAATAG-GCTGA-AATAAAAGATCATAATGGGGAATA
3207442 CGTAGTTCTA
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
66 16 0.16
67 79 0.80
68 4 0.04
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (67 bp):
AGACAAACTGATAATAGGCTGAAATAAAAGATCATAATGGGGAATATGCAGCTTCCATCAACAGC
TG
Found at i:3210998 original size:20 final size:19
Alignment explanation
Indices: 3210943--3210998 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3210933 AAAACCCTTA
*
3210943 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
3210963 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
3210983 AATGTATCGATACATG
1 AAAGTATCGATACATG
3210999 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:3211086 original size:13 final size:13
Alignment explanation
Indices: 3211068--3211093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3211058 TACACAAAAT
3211068 ATGTATCGATACA
1 ATGTATCGATACA
3211081 ATGTATCGATACA
1 ATGTATCGATACA
3211094 CAAAAAAATT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3211091 original size:32 final size:34
Alignment explanation
Indices: 3211050--3211114 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
3211040 TAGCCAAACT
*
3211050 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
3211082 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
3211115 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:3215180 original size:15 final size:15
Alignment explanation
Indices: 3215160--3215190 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3215150 TAAAAATATC
*
3215160 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3215175 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3215190 C
1 C
3215191 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3217289 original size:13 final size:13
Alignment explanation
Indices: 3217271--3217321 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
3217261 CATTTTTCTT
3217271 TGTATCGATACAA
1 TGTATCGATACAA
3217284 TGTATCGATACAA
1 TGTATCGATACAA
*
3217297 TGTATCGATACAC
1 TGTATCGATACAA
*
3217310 TATATCGATACA
1 TGTATCGATACA
3217322 GGGGGATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3217476 original size:20 final size:20
Alignment explanation
Indices: 3217433--3217478 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3217423 AAATCTTTTA
3217433 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3217454 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3217474 CAAAA
1 CAAAA
3217479 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3219748 original size:20 final size:19
Alignment explanation
Indices: 3219693--3219748 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3219683 AAAACCCTTA
*
3219693 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
3219713 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
3219733 AATGTATCGATACATG
1 AAAGTATCGATACATG
3219749 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:3219836 original size:13 final size:13
Alignment explanation
Indices: 3219818--3219843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3219808 TACACAAAAT
3219818 ATGTATCGATACA
1 ATGTATCGATACA
3219831 ATGTATCGATACA
1 ATGTATCGATACA
3219844 CAAAAAAAAT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3219841 original size:32 final size:33
Alignment explanation
Indices: 3219800--3219864 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
3219790 TAGCCAAACT
*
3219800 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAAATGTATCGATACAA
3219832 TGTATCGATACACAAAAAAAATGTATCGATACA
1 TGTATCGATACAC-AAAAAAATGTATCGATACA
3219865 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
34 17 0.57
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (33 bp):
TGTATCGATACACAAAAAAATGTATCGATACAA
Found at i:3222073 original size:79 final size:77
Alignment explanation
Indices: 3221865--3222386 Score: 310
Period size: 80 Copynumber: 6.6 Consensus size: 77
3221855 TAAAGCACTG
* * * * * ** * *
3221865 AATTTTTTATCTTTAGGATATTCCAACCCCACCATCTTTAAGGGGATACTTTAACCTTATTTCTA
1 AATTTTTCATCTCTGGGATACTCCAACCCCACCATCTCTAAGGGGATACTCCAACCTCATTTTTA
*
3221930 CTTCCAAAATGCCA
66 CTTCTAAAA--CCA
* * * * * * *
3221944 AATTTTTTATTTCTAGGGATACTCCAGCCCCACCATATTTGAGGCGATACTCCAACCTCATTTTT
1 AATTTTTCATCTCT-GGGATACTCCAACCCCACCATCTCTAAGGGGATACTCCAACCTCATTTTT
3222009 ACTTCTTAAAAGCCA
65 ACTTC-TAAAA-CCA
* * * * *
3222024 AATTTTTCATCTCTGGGATATTCTAGCCCCACCATCTCTAAGGGGATACTCCAACCACGTTTTTA
1 AATTTTTCATCTCTGGGATACTCCAACCCCACCATCTCTAAGGGGATACTCCAACCTCATTTTTA
*
3222089 CTTC--CAACC-
66 CTTCTAAAACCA
* * * * * *
3222098 ---TATCCATCTTTGAGGATACTCCAA-CCTATCCATCTCTAAGGGGATACTCCGATCTCATTTT
1 AATTTTTCATCTCTG-GGATACTCCAACCCCA-CCATCTCTAAGGGGATACTCCAACCTCATTTT
*
3222159 TACTTCTAAAACACTG
64 TACTTCTAAAAC-C-A
* * * * * *
3222175 AATTTTTCATCTCGGGGATACTCTAACCTCACCTTCTCCAAGAGGATACTCCAACC-CTATTTTT
1 AATTTTTCATCTCTGGGATACTCCAACCCCACCATCTCTAAGGGGATACTCCAACCTC-A--TTT
*
3222239 TTACTTCTAAAACATCG
63 TTACTTCTAAAAC--CA
* * ** * * *
3222256 AATTTTTGATCT-TGGGGGATATTCCAA-CCCGTCATCTCTGAA-GGAATGCTCCAACCCCATTT
1 AATTTTTCATCTCT--GGGATACTCCAACCCCACCATCTCT-AAGGGGATACTCCAACCTCA-TT
* ***
3222318 TTTACTTCCACAATATTG
62 TTTACTTCTA-AA-ACCA
* * **
3222336 AATTCTTCATCTTTAGGGATACTCCAACCTTACCATCTCTAAGGGGATACT
1 AATTTTTCATCTCT-GGGATACTCCAACCCCACCATCTCTAAGGGGATACT
3222387 TTAACCTTGG
Statistics
Matches: 343, Mismatches: 74, Indels: 50
0.73 0.16 0.11
Matches are distributed among these distances:
71 12 0.03
72 42 0.12
74 3 0.01
75 3 0.01
76 2 0.01
78 1 0.00
79 90 0.26
80 107 0.31
81 68 0.20
82 15 0.04
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (77 bp):
AATTTTTCATCTCTGGGATACTCCAACCCCACCATCTCTAAGGGGATACTCCAACCTCATTTTTA
CTTCTAAAACCA
Found at i:3222308 original size:81 final size:80
Alignment explanation
Indices: 3222111--3222374 Score: 198
Period size: 81 Copynumber: 3.3 Consensus size: 80
3222101 CCATCTTTGA
* * * * * * *
3222111 GGATACTCCAACCT-ATCCATCTCTAAGGGGATACTCCGATCTCA-TTTTTACTTCTAAAACACT
1 GGATACTCCAACCTCA-CCTTCTCCAAGAGAATACTCCAACCCCATTTTTTACTTCTAAAACACT
3222174 GAATTTTTCATCTCGG
65 GAATTTTTCATCTCGG
* * *
3222190 GGATACTCTAACCTCACCTTCTCCAAGAGGATACTCCAACCCTATTTTTTTACTTCTAAAACA-T
1 GGATACTCCAACCTCACCTTCTCCAAGAGAATACTCCAACCCCA-TTTTTTACTTCTAAAACACT
* *
3222254 CGAATTTTTGATCTTGGG
65 -GAATTTTTCATC-TCGG
* * * * * * * *
3222272 GGATATTCCAACCCGTCATC-TCT-GAAG-GAATGCTCCAACCCCATTTTTTACTTCCACAATAT
1 GGATACTCCAA-CC-TCACCTTCTCCAAGAGAATACTCCAACCCCATTTTTTACTTCTAAAACAC
* **
3222334 TGAATTCTTCATCTTTAG
64 TGAATTTTTCATC-TCGG
* *
3222352 GGATACTCCAACCTTACCATCTC
1 GGATACTCCAACCTCACCTTCTC
3222375 TAAGGGGATA
Statistics
Matches: 148, Mismatches: 27, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
78 3 0.02
79 39 0.26
80 40 0.27
81 42 0.28
82 15 0.10
83 5 0.03
84 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.34
Consensus pattern (80 bp):
GGATACTCCAACCTCACCTTCTCCAAGAGAATACTCCAACCCCATTTTTTACTTCTAAAACACTG
AATTTTTCATCTCGG
Found at i:3228309 original size:24 final size:24
Alignment explanation
Indices: 3228273--3228319 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3228263 CCGATTACAC
3228273 ATTTTGTGCATTCACTA-GTGGCAT
1 ATTTTGTGCATTCA-TAGGTGGCAT
*
3228297 ATTTTGTGTATTCATAGGTGGCA
1 ATTTTGTGCATTCATAGGTGGCA
3228320 GGTTCTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (24 bp):
ATTTTGTGCATTCATAGGTGGCAT
Found at i:3231738 original size:15 final size:15
Alignment explanation
Indices: 3231718--3231748 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3231708 ATTAAATACC
3231718 AATTAAAATTGAATT
1 AATTAAAATTGAATT
*
3231733 AATTAAAATTTAATT
1 AATTAAAATTGAATT
3231748 A
1 A
3231749 GCATGTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
AATTAAAATTGAATT
Found at i:3233124 original size:293 final size:295
Alignment explanation
Indices: 3232574--3233162 Score: 952
Period size: 293 Copynumber: 2.0 Consensus size: 295
3232564 TTAACCTAGA
* * *
3232574 GACATTGCCTTGTTTTTCTAAAAAAAAATTAATTAAAAATATTAGAGAAATATTCCTCCTATACC
1 GACATTGCCTTGCTTTTCTAAAAAAAAATTAATTAAAAATATTAGAGAAATATT-CTCCAAGACC
* * * * * *
3232639 TAAAACGATCTAAAATGATGAATCTAATCTTAAATGTATAGCTTTGGTATGGAAACGACCCGATG
65 TAAAACGATCTAAAATGATGAACCTAATCCTAAATATACACCTTTGGCATGGAAACGACCCGATG
*
3232704 ACGACCTAAAACTTAATTCTAGAGAAATTATGAAAATACCCCTGGGATATATCTTCGACATGAAA
130 ACGACCTAAAACTTAATTCTAGAGAAATTATGAAAATACCCCTGGGATATACCTTCGACATGAAA
* * *
3232769 TTATGTCGATAACCTTAAATGACACAAAAATATTATGTAATAATAACTTTTACCTTTTTAGAGAA
195 TTATCTCGATAACCCTAAATGACACAAAAATATTATGAAATAATAACTTTTACCTTTTTAGAGAA
3232834 CTAAGGGAATACAAAAGTTTTTTAATATTTTTAACAT
260 CTAAGGGAATACAAAAG-TTTTTAATATTTTTAACAT
3232871 GACATTGCCTTGCTTTTCT-AAAAAAAATTAATTAAAAATATTAGAGAAATA-T-TCCAAGACCT
1 GACATTGCCTTGCTTTTCTAAAAAAAAATTAATTAAAAATATTAGAGAAATATTCTCCAAGACCT
*
3232933 AAAACGATCTAAAATGATGAACCTAATCCTAAATATACACCTTTGGCATGGAAGCGACCCGATGA
66 AAAACGATCTAAAATGATGAACCTAATCCTAAATATACACCTTTGGCATGGAAACGACCCGATGA
* * **
3232998 CGACCTAAGACTTAATTCTAGAGAAATTATGAAAATGCTTCTGGGATATACCTTCGACATGGAAA
131 CGACCTAAAACTTAATTCTAGAGAAATTATGAAAATACCCCTGGGATATACCTTCGACAT-GAAA
*
3233063 -TATCTCGATAACCCTAAATGACATAAAAATATTATGAAATAATAACTTTTACCTTTTTAGAGAA
195 TTATCTCGATAACCCTAAATGACACAAAAATATTATGAAATAATAACTTTTACCTTTTTAGAGAA
3233127 CTAAGGGAATACAAAAGTTTTTAATATTTTTAACAT
260 CTAAGGGAATACAAAAGTTTTTAATATTTTTAACAT
3233163 CGCACCGGAG
Statistics
Matches: 272, Mismatches: 19, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
292 19 0.07
293 198 0.73
294 4 0.01
295 1 0.00
296 32 0.12
297 18 0.07
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (295 bp):
GACATTGCCTTGCTTTTCTAAAAAAAAATTAATTAAAAATATTAGAGAAATATTCTCCAAGACCT
AAAACGATCTAAAATGATGAACCTAATCCTAAATATACACCTTTGGCATGGAAACGACCCGATGA
CGACCTAAAACTTAATTCTAGAGAAATTATGAAAATACCCCTGGGATATACCTTCGACATGAAAT
TATCTCGATAACCCTAAATGACACAAAAATATTATGAAATAATAACTTTTACCTTTTTAGAGAAC
TAAGGGAATACAAAAGTTTTTAATATTTTTAACAT
Found at i:3238251 original size:21 final size:20
Alignment explanation
Indices: 3238225--3238280 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
3238215 AATTATACGA
3238225 ATTTAAATTT-TTTTAAATATG
1 ATTTAAATTTATTTTAAA-A-G
*
3238246 ATTTAATTTTATTTGTAAAAG
1 ATTTAAATTTATTT-TAAAAG
*
3238267 -TTTAAATTTGTTTT
1 ATTTAAATTTATTTT
3238281 CTGGTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 11 0.37
21 10 0.33
22 4 0.13
23 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTTAAATTTATTTTAAAAG
Found at i:3238262 original size:74 final size:74
Alignment explanation
Indices: 3238046--3238410 Score: 388
Period size: 74 Copynumber: 5.0 Consensus size: 74
3238036 TCAACTAAGT
* * * *
3238046 AGTTTAAATTT-ATTTTGGGTATAATTATA-GAAGTTTAAAATTTTTTAAGGTATAATTTATTTT
1 AGTTTAAATTTGTTTTTGAGTATAATTATACG-AGTTTAAAATTTTTTAAGATATGATTTATTTT
3238109 TATTTGTAAA
65 TATTTGTAAA
* * * * * *
3238119 AGTATAGATTTGTTATTT-AGTTTGATTATACGAGTTT-AAA-TTTTTAAGATATTATTTAATTT
1 AGTTTAAATTTGTT-TTTGAGTATAATTATACGAGTTTAAAATTTTTTAAGATATGATTTATTTT
* *
3238181 TACTTGTAGA
65 TATTTGTAAA
* * * * *
3238191 CGTTCAAATTTGTTTTTCGAGTATAATTATACGAATTTAAATTTTTTTAA-ATATGATTTAATTT
1 AGTTTAAATTTGTTTTT-GAGTATAATTATACGAGTTTAAAATTTTTTAAGATATGATTTATTTT
3238255 TATTTGTAAA
65 TATTTGTAAA
* *
3238265 AGTTTAAATTTGTTTTCTG-GTTTAATTATATGAGTTTAAAATTTTTTAAGATATGATTTATTTT
1 AGTTTAAATTTGTTTT-TGAGTATAATTATACGAGTTTAAAATTTTTTAAGATATGATTTATTTT
3238329 TATTTGTAAA
65 TATTTGTAAA
* * * * * * *
3238339 AATTTAAATTTGTTTTTTATGT-TGATTATAGGAGTTT-AATTTTTTTACGATATGCTTTATTTT
1 AGTTTAAATTTGTTTTTGA-GTATAATTATACGAGTTTAAAATTTTTTAAGATATGATTTATTTT
3238402 TATTTGTAA
65 TATTTGTAA
3238411 GATTAATTTA
Statistics
Matches: 245, Mismatches: 36, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
71 3 0.01
72 37 0.15
73 87 0.36
74 104 0.42
75 14 0.06
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (74 bp):
AGTTTAAATTTGTTTTTGAGTATAATTATACGAGTTTAAAATTTTTTAAGATATGATTTATTTTT
ATTTGTAAA
Found at i:3238693 original size:120 final size:121
Alignment explanation
Indices: 3238558--3238802 Score: 348
Period size: 121 Copynumber: 2.0 Consensus size: 121
3238548 AATCAGAGCT
* * *
3238558 ATGAGGAAAATAGTTGAATTTTAGTTTGAAAGGATTAAACCGTTTGAATA-TTTAGAAGTATGAT
1 ATGAGGAAAAGAGTTGAATTTTAGTTTGAAAGGATTAAACCGTTTGAATATTTTAAAAGTATAAT
* * * ** *
3238622 TTATTTTTATTTATGAAAATTTAGTTTAATTTTTATTTGGGGAATGTTGAATTTAA
66 TTATATCTATATATGAAAATTTAGTTTAATTTTTATTTACGGAATGATGAATTTAA
* * *
3238678 ATGAGGAGAAGAGTTGAATTTTAGTTTGAAGGGATTAAACTGTTTGAATATTTTAAAAGTATAAT
1 ATGAGGAAAAGAGTTGAATTTTAGTTTGAAAGGATTAAACCGTTTGAATATTTTAAAAGTATAAT
* * *
3238743 TTATATCTATATGTGAAAATTTAGTTTAATTTTTGTTTACGTAATGATGAATTTAA
66 TTATATCTATATATGAAAATTTAGTTTAATTTTTATTTACGGAATGATGAATTTAA
3238799 ATGA
1 ATGA
3238803 AAATCATTAT
Statistics
Matches: 109, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
120 46 0.42
121 63 0.58
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (121 bp):
ATGAGGAAAAGAGTTGAATTTTAGTTTGAAAGGATTAAACCGTTTGAATATTTTAAAAGTATAAT
TTATATCTATATATGAAAATTTAGTTTAATTTTTATTTACGGAATGATGAATTTAA
Found at i:3242245 original size:104 final size:102
Alignment explanation
Indices: 3242083--3242274 Score: 246
Period size: 104 Copynumber: 1.9 Consensus size: 102
3242073 TTATAGTTAC
* *
3242083 AAGGCGAGGTTGGAGTATCCCCTCGGAAAGATGGGGTTGGAGTATTCCCGTGGATGACAAATAAT
1 AAGGCGAGGTTGGAGTATCCCCTCAGAAAGATGGGGTTGGAGTATTCCCATGGATGACAAATAAT
3242148 TTTGATA-AAAAGAAAAGTGTTAAATTTTGACAATTCTGA
66 TTT-A-ACAAAAGAAAAGT-TTAAATTTTGACAATTCTGA
* * * * *
3242187 AAGGCGGGGTTGGAGTATCCCTTTAG-AAGGTCGGGGTTGGAGTA-TCTCCATGGATGACAAATG
1 AAGGCGAGGTTGGAGTATCCCCTCAGAAAGAT-GGGGTTGGAGTATTC-CCATGGATGACAAATA
*
3242250 ATTTTAACAAAGGAAAAGTTTAAAT
64 ATTTTAACAAAAGAAAAGTTTAAAT
3242275 CTTAACAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
102 7 0.09
103 17 0.22
104 53 0.69
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (102 bp):
AAGGCGAGGTTGGAGTATCCCCTCAGAAAGATGGGGTTGGAGTATTCCCATGGATGACAAATAAT
TTTAACAAAAGAAAAGTTTAAATTTTGACAATTCTGA
Found at i:3242330 original size:103 final size:105
Alignment explanation
Indices: 3242095--3242335 Score: 255
Period size: 103 Copynumber: 2.3 Consensus size: 105
3242085 GGCGAGGTTG
* *
3242095 GAGTATCCCCTCGGAAAGAT-GGGGTTGGAGTAT-TCCCGTGGATGACAAATAATTTTGATAAAA
1 GAGTATCCCCTC-GAAAGGTCGGGGTTGGAGTATCTCCCATGGATGACAAATAATTTTGATAAAA
* * * * * *
3242158 AGAAAAGTGTTAAATTTTGACAATTCTGAAAGGCGGGGTTG
65 AGAAAAGTGTTAAATCTTAACAATTCTCAAAGGCAGGGATA
** *
3242199 GAGTAT-CCCTTTAGAAGGTCGGGGTTGGAGTATCT-CCATGGATGACAAATGATTTT-A-ACAA
1 GAGTATCCCCTCGA-AAGGTCGGGGTTGGAGTATCTCCCATGGATGACAAATAATTTTGATA-AA
* *
3242260 AGGAAAAGT-TTAAATCTTAACAAATT-TCAAAGAGTAGGGATA
64 AAGAAAAGTGTTAAATCTTAAC-AATTCTCAAAG-GCAGGGATA
*
3242302 GAGTATCCCCTCGAAAGGTCAGGGTTGGAGTATC
1 GAGTATCCCCTCGAAAGGTCGGGGTTGGAGTATC
3242336 CTCGTGAATA
Statistics
Matches: 114, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
102 17 0.15
103 53 0.46
104 43 0.38
105 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (105 bp):
GAGTATCCCCTCGAAAGGTCGGGGTTGGAGTATCTCCCATGGATGACAAATAATTTTGATAAAAA
GAAAAGTGTTAAATCTTAACAATTCTCAAAGGCAGGGATA
Found at i:3244839 original size:20 final size:20
Alignment explanation
Indices: 3244814--3244868 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3244804 ACATTTCAAG
* *
3244814 TATGTATCGATACATTTACT
1 TATGTATCAATACATTAACT
3244834 TATGTATCAATACATTAACT
1 TATGTATCAATACATTAACT
*
3244854 TATTGCATCAATACA
1 TA-TGTATCAATACA
3244869 AATTATAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (20 bp):
TATGTATCAATACATTAACT
Found at i:3245665 original size:41 final size:40
Alignment explanation
Indices: 3245614--3245736 Score: 106
Period size: 41 Copynumber: 3.2 Consensus size: 40
3245604 ACCCAAAAAT
3245614 AAATTTAAACTTTTATAAATAAAAATAAATCATTTCTTAAA
1 AAATTTAAACTTTTATAAATAAAAATAAATCA-TTCTTAAA
** *
3245655 AAATTTAAACTCATAT-AATCAAACAA-AAA--A--C----C
1 AAATTTAAACTTTTATAAAT-AAA-AATAAATCATTCTTAAA
3245687 AAATTTAAACTTTTATAAAT-AAAATAAATCATATCTTAAA
1 AAATTTAAACTTTTATAAATAAAAATAAATCAT-TCTTAAA
3245727 AAATTTAAAC
1 AAATTTAAAC
3245737 ACTTATAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 27
0.66 0.06 0.28
Matches are distributed among these distances:
30 2 0.03
31 5 0.08
32 14 0.22
33 4 0.06
36 2 0.03
39 1 0.02
40 13 0.21
41 20 0.32
42 2 0.03
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (40 bp):
AAATTTAAACTTTTATAAATAAAAATAAATCATTCTTAAA
Found at i:3245708 original size:73 final size:71
Alignment explanation
Indices: 3245608--3245888 Score: 320
Period size: 72 Copynumber: 3.9 Consensus size: 71
3245598 TATTTAACCC
* *
3245608 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATCATTTCTTAAAAAATTTAAACTCATATAA
1 AAAAACAAATTTAAACTTTTATAAATAAAAATAAATCATATCTT-AAAAATTTAAACTCATATAA
3245673 TCAAACA
65 TCAAACA
* *
3245680 AAAAACCAAATTTAAACTTTTATAAAT-AAAATAAATCATATCTTAAAAAATTTAAACACTTATA
1 AAAAA-CAAATTTAAACTTTTATAAATAAAAATAAATCATATCTT-AAAAATTTAAACTCATATA
3245744 ATCATAACTA
64 ATCA-AAC-A
* * * * * *
3245754 GAAAACAAATTTAAA-TTTT-TACAA-AAAAATAAATAATACCTTAAAATTTTAAA-TCCTATCA
1 AAAAACAAATTTAAACTTTTATA-AATAAAAATAAATCATATCTTAAAAATTTAAACTCATATAA
3245815 TCAAACCA
65 TCAAA-CA
* * * * * *
3245823 AAATACAAATTTAAACTTATACAAGTAAAAATAAATTATATCTTAAAAATTTAATCTCATATAAT
1 AAAAACAAATTTAAACTTTTATAAATAAAAATAAATCATATCTTAAAAATTTAAACTCATATAAT
3245888 C
66 C
3245889 GTATCCAAAA
Statistics
Matches: 177, Mismatches: 22, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
69 16 0.09
70 13 0.07
71 38 0.21
72 72 0.41
73 33 0.19
74 5 0.03
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.33
Consensus pattern (71 bp):
AAAAACAAATTTAAACTTTTATAAATAAAAATAAATCATATCTTAAAAATTTAAACTCATATAAT
CAAACA
Found at i:3245836 original size:142 final size:146
Alignment explanation
Indices: 3245609--3245876 Score: 352
Period size: 142 Copynumber: 1.9 Consensus size: 146
3245599 ATTTAACCCA
* * **
3245609 AAAATAAATTTAAACTTTTATAAATAAAAATAAATCATTTCTTAAAAAATTTAAACTCATATAAT
1 AAAACAAATTTAAACTTTTATAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCATATAAT
* *
3245674 CAAACAAAAAACCAAATTTAAACTTTTATAAAT-AAAATAAATCATATCTTAAAAAATTTAAACA
66 CAAACAAAAAACCAAATTTAAACTTATACAAATAAAAATAAATCATATCTT-AAAAATTTAAACA
3245738 CTTATAATCATAACTAG
130 CTTATAATCATAACTAG
* * *
3245755 AAAACAAATTTAAA-TTTT-TACAA-AAAAATAAATAATACCTT-AAAATTTTAAA-TCCTATCA
1 AAAACAAATTTAAACTTTTATA-AATAAAAATAAATAATACCTTAAAAAATTTAAACTCATATAA
* * *
3245815 TCAAACCAAAATA-CAAATTTAAACTTATACAAGTAAAAATAAATTATATCTTAAAAATTTAA
65 TCAAA-CAAAAAACCAAATTTAAACTTATACAAATAAAAATAAATCATATCTTAAAAATTTAA
3245877 TCTCATATAA
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
142 39 0.36
143 32 0.30
144 17 0.16
145 6 0.06
146 13 0.12
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (146 bp):
AAAACAAATTTAAACTTTTATAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCATATAAT
CAAACAAAAAACCAAATTTAAACTTATACAAATAAAAATAAATCATATCTTAAAAATTTAAACAC
TTATAATCATAACTAG
Found at i:3246190 original size:70 final size:70
Alignment explanation
Indices: 3246049--3246232 Score: 208
Period size: 70 Copynumber: 2.6 Consensus size: 70
3246039 AAATCAACTT
* * * * *
3246049 TAAAATAATTTAAACTCCTATAATCAACCTAAAAGATAAATTTAAATTTTTAAAAATTAAAATGA
1 TAAAA-AATTTAAACTCATATAATCAA-ATTAAA-A-AAATTTAAACTTTTAAAAATAAAAATGA
3246114 ATCATATCA
62 ATCATATCA
* *
3246123 TAAAAAATTTAAACTCGTATAATCAAATTAAAAAAATTTAAACTTTTACAAATAAAAAT-ATATC
1 TAAAAAATTTAAACTCATATAATCAAATTAAAAAAATTTAAACTTTTAAAAATAAAAATGA-ATC
*
3246187 ATATCT
65 ATATCA
* * *
3246193 TATAAAATTTAAACTCATATAATCATATTCAAAAATATTT
1 TAAAAAATTTAAACTCATATAATCAAATT-AAAAAAATTT
3246233 TTACAAATAA
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
69 1 0.01
70 57 0.59
71 10 0.10
72 4 0.04
73 20 0.21
74 5 0.05
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (70 bp):
TAAAAAATTTAAACTCATATAATCAAATTAAAAAAATTTAAACTTTTAAAAATAAAAATGAATCA
TATCA
Found at i:3246244 original size:65 final size:67
Alignment explanation
Indices: 3246016--3246248 Score: 190
Period size: 70 Copynumber: 3.4 Consensus size: 67
3246006 TTCAAAAATC
* * * * *
3246016 AAATTAA-TCTTACAAATAGAAATAAATCA-A-CTTTAAAATAATTTAAACTCCTATAATCAACC
1 AAATTAATTTTTACAAATAAAAAT-AATCATATC-TTATAA-AATTTAAACTCATATAATCAA-A
*
3246078 TAAAAGA
62 TTAAA-A
* * * * *
3246085 TAAATTTAAATTTTTAAAAATTAAAATGAATCATATCATAAAAAATTTAAACTCGTATAATCAAA
1 -AAA-TT-AATTTTTACAAATAAAAAT-AATCATATCTTATAAAATTTAAACTCATATAATCAAA
3246150 TTAAAA
62 TTAAAA
* *
3246156 AAATTTAAACTTTTACAAATAAAAATATATCATATCTTATAAAATTTAAACTCATATAATCATAT
1 AAA-TT-AATTTTTACAAATAAAAATA-ATCATATCTTATAAAATTTAAACTCATATAATCAAAT
*
3246221 T-CAA
63 TAAAA
3246225 AAA-T-ATTTTTACAAATAAAAATAA
1 AAATTAATTTTTACAAATAAAAATAA
3246249 ATAATACTTT
Statistics
Matches: 139, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
64 1 0.01
65 18 0.13
67 1 0.01
69 6 0.04
70 60 0.43
71 3 0.02
72 6 0.04
73 37 0.27
74 6 0.04
75 1 0.01
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (67 bp):
AAATTAATTTTTACAAATAAAAATAATCATATCTTATAAAATTTAAACTCATATAATCAAATTAA
AA
Found at i:3246569 original size:15 final size:17
Alignment explanation
Indices: 3246551--3246583 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3246541 CCCGTGACAC
3246551 TAATTT-TTT-AAAATT
1 TAATTTATTTCAAAATT
3246566 TAATTTATTTCAAAATT
1 TAATTTATTTCAAAATT
3246583 T
1 T
3246584 TTTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTTATTTCAAAATT
Found at i:3246685 original size:18 final size:17
Alignment explanation
Indices: 3246662--3246695 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3246652 AAGAAATCGA
3246662 TAATTTAATATAATTTTT
1 TAATTTAAT-TAATTTTT
*
3246680 TAATTTAGTTAATTTT
1 TAATTTAATTAATTTT
3246696 AAAATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TAATTTAATTAATTTTT
Found at i:3246889 original size:27 final size:27
Alignment explanation
Indices: 3246845--3246896 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3246835 TTCAATAAAA
* **
3246845 TATAAAAAATATTTTTTAAAAAATATT
1 TATAAAAAACATAGTTTAAAAAATATT
*
3246872 TATAAAAAACATAGTTTAAGAAATA
1 TATAAAAAACATAGTTTAAAAAATA
3246897 AAAAAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
TATAAAAAACATAGTTTAAAAAATATT
Found at i:3247450 original size:2 final size:2
Alignment explanation
Indices: 3247443--3247504 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
3247433 CAACTTGCTT
* *
3247443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3247485 TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3247505 GCGCACACGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3250287 original size:2 final size:2
Alignment explanation
Indices: 3250282--3250317 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3250272 ATATATATAT
3250282 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3250318 GGAATTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3251649 original size:16 final size:18
Alignment explanation
Indices: 3251621--3251654 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3251611 CAGTTAATTC
3251621 ATATAATTATTTT-TAAA
1 ATATAATTATTTTATAAA
3251638 ATATAA-TATTTTATAAA
1 ATATAATTATTTTATAAA
3251655 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATAATTATTTTATAAA
Found at i:3254107 original size:17 final size:18
Alignment explanation
Indices: 3254075--3254110 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3254065 AAAACGTAAA
*
3254075 AATAAATATGTTTAAAAT
1 AATAAAAATGTTTAAAAT
3254093 AATAAAAAT-TTTAAAAT
1 AATAAAAATGTTTAAAAT
3254110 A
1 A
3254111 TGAGAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AATAAAAATGTTTAAAAT
Found at i:3254518 original size:23 final size:23
Alignment explanation
Indices: 3254471--3254518 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3254461 TCTATCAAAC
* *
3254471 ATCAAAATTTTGTCTCATCTTCT
1 ATCAAAATTTTGTCTCATATGCT
* *
3254494 ATCAAAATTTTTTCTCTTATGCT
1 ATCAAAATTTTGTCTCATATGCT
3254517 AT
1 AT
3254519 TAATTTCCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.19, G:0.04, T:0.50
Consensus pattern (23 bp):
ATCAAAATTTTGTCTCATATGCT
Found at i:3256268 original size:2 final size:2
Alignment explanation
Indices: 3256261--3256315 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
3256251 TTTAATCAAT
** *
3256261 TA TA TA TA TA TA TA TA TA TA -A CG TA CA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3256301 TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
3256316 CAGTAAGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3258037 original size:2 final size:2
Alignment explanation
Indices: 3258030--3258062 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3258020 TTATTTTTCT
3258030 TA 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 TA T
3258063 TTCTGACAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3259522 original size:2 final size:2
Alignment explanation
Indices: 3259515--3259546 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3259505 TTCACCCATC
3259515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3259547 AATTTATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3262071 original size:3 final size:3
Alignment explanation
Indices: 3262063--3262102 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3262053 TCAAGTATTG
3262063 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3262103 GACTTTGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3262228 original size:18 final size:19
Alignment explanation
Indices: 3262189--3262228 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3262179 ATTTAGTATT
*
3262189 AATTTTTATGTATATTATA
1 AATTTTTAAGTATATTATA
*
3262208 AATTTTTAAGTTTATTA-A
1 AATTTTTAAGTATATTATA
3262226 AAT
1 AAT
3262229 ACATCATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
AATTTTTAAGTATATTATA
Found at i:3264432 original size:13 final size:13
Alignment explanation
Indices: 3264414--3264439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3264404 TCTGTCCCTT
3264414 CAGCACCTCATTA
1 CAGCACCTCATTA
3264427 CAGCACCTCATTA
1 CAGCACCTCATTA
3264440 ATTTCTTCAT
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:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
CAGCACCTCATTA
Found at i:3266369 original size:28 final size:30
Alignment explanation
Indices: 3266320--3266377 Score: 102
Period size: 28 Copynumber: 2.0 Consensus size: 30
3266310 AATCGATGAT
3266320 TAGAAAATAAATCGGGATTGGAGTATCCCC
1 TAGAAAATAAATCGGGATTGGAGTATCCCC
3266350 TAGAAAAT-AA-CGGGATTGGAGTATCCCC
1 TAGAAAATAAATCGGGATTGGAGTATCCCC
3266378 AATTATGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 18 0.64
29 2 0.07
30 8 0.29
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (30 bp):
TAGAAAATAAATCGGGATTGGAGTATCCCC
Found at i:3266467 original size:28 final size:28
Alignment explanation
Indices: 3266411--3266487 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
3266401 GGAATAAAGC
*** *
3266411 CGGGGTTAGAGTATCCCCTCGGAAGTAA
1 CGGGGTTAGAGTATCCCCGATGAAATAA
*
3266439 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTAGAGTATCCCCGATGAAATAA
* * *
3266467 CGAGGTTCGAGTATCCTCGAT
1 CGGGGTTAGAGTATCCCCGAT
3266488 TATGAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (28 bp):
CGGGGTTAGAGTATCCCCGATGAAATAA
Found at i:3266534 original size:52 final size:51
Alignment explanation
Indices: 3266475--3266856 Score: 251
Period size: 51 Copynumber: 7.3 Consensus size: 51
3266465 AACGAGGTTC
* * * *
3266475 GAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAATCGGAGTTG
* * * *
3266527 GAGTATCCCCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAA-CCGAGGTTG
1 GAGTATCCCCGATT--ATGAAAAATTAGTGTTTTGGAAATAAAATCGGA-GTTG
** * * * *
3266580 GAGTATCCTTGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGGGGTTG
1 GAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAATCGGAGTTG
* * * * * *
3266632 GAGTATCCCCGATTATGAAAAATCAATATTTTGGAGATAAAGTCGGGGTTG
1 GAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGGAGTTG
* ** * *
3266683 GAGTATCCCC--TCA-GAAATAA-T-G-GGGTTGGAGTATCCCCGATGATTAA-CGGGGTTG
1 GAGTATCCCCGATTATGAAA-AATTAGTGTTTTGGA--A------AT-A-AAATCGGAGTTG
* *
3266738 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGGAAATAAAATCGGAGTTG
*
3266792 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAATCGGAGTTG
* *
3266843 AAATATCCCCGATT
1 GAGTATCCCCGATT
3266857 GTGGAGAATT
Statistics
Matches: 257, Mismatches: 46, Indels: 55
0.72 0.13 0.15
Matches are distributed among these distances:
46 5 0.02
48 4 0.02
49 4 0.02
51 72 0.28
52 55 0.21
53 41 0.16
54 38 0.15
55 21 0.08
56 1 0.00
57 1 0.00
58 5 0.02
59 2 0.01
60 1 0.00
61 2 0.01
63 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGGAGTTG
Found at i:3266742 original size:27 final size:28
Alignment explanation
Indices: 3266675--3266750 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
3266665 GAGATAAAGT
*
3266675 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
* *
3266703 TGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
3266730 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3266751 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:3267822 original size:46 final size:46
Alignment explanation
Indices: 3267769--3267860 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
3267759 ACATCTATTG
3267769 GACAAAGGAGATTTTTTGTTGAAAAAAACATCATTATGGAGATTAT
1 GACAAAGGAGATTTTTTGTTGAAAAAAACATCATTATGGAGATTAT
3267815 GACAAAGGAGATTTTTTGTTGAAAAAAACATCATTATGGAGATTAT
1 GACAAAGGAGATTTTTTGTTGAAAAAAACATCATTATGGAGATTAT
3267861 CTTACCATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (46 bp):
GACAAAGGAGATTTTTTGTTGAAAAAAACATCATTATGGAGATTAT
Found at i:3269350 original size:13 final size:13
Alignment explanation
Indices: 3269332--3269356 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3269322 TAGCTAATTA
3269332 TGTATCGATACAT
1 TGTATCGATACAT
3269345 TGTATCGATACA
1 TGTATCGATACA
3269357 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3271160 original size:17 final size:17
Alignment explanation
Indices: 3271138--3271188 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
3271128 TTGCATTAGG
3271138 ATAGACATGATAGCACC
1 ATAGACATGATAGCACC
3271155 ATAGACATGATAGCACC
1 ATAGACATGATAGCACC
*
3271172 ATAGACATAATAGCACC
1 ATAGACATGATAGCACC
3271189 TAGGCATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (17 bp):
ATAGACATGATAGCACC
Found at i:3277070 original size:32 final size:32
Alignment explanation
Indices: 3277021--3277718 Score: 1128
Period size: 32 Copynumber: 21.8 Consensus size: 32
3277011 AAAATGGTGA
* * **
3277021 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277053 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
3277085 TTTGAAAAGGGTCGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
3277117 TTTGAAATGAGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
3277149 TTTGGAATGGGTTGCCACTAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3277181 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277213 TTTGAAATGGGTTGCCACCGACTTGTGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277245 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277277 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3277309 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277341 TTTGAAATGGGTTGCCATCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3277373 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277405 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277437 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277469 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277501 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
3277533 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277565 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
3277597 TTTGGAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
3277629 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
3277661 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
3277693 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
3277719 GTCTTAAAAG
Statistics
Matches: 626, Mismatches: 40, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
31 13 0.02
32 613 0.98
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:3278142 original size:164 final size:162
Alignment explanation
Indices: 3277701--3278575 Score: 1345
Period size: 164 Copynumber: 5.3 Consensus size: 162
3277691 GCTTTGAAAT
* * *
3277701 GGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCATG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
* ** * *
3277766 AAGTTGTGGTTTTAAAAGGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGA
65 GAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
*
3277831 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAATA
129 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
3277865 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTACCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
3277930 AGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
* *
3277995 TAAAAGGGTGCCACAGAGTTGTGGTCTTAAAA
131 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* ** *
3278027 GGGATGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTTTTAAAAGGGATGCCAT
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCAC
* *
3278092 AGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
64 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
3278157 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
129 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
3278191 GGGTGCCACGGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCAC
1 GGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCAC
* *
3278256 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGT
64 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
*
3278321 CTTAAAAGGGATGCCACGGAGTTGTAGACTTAAAA
129 CTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAA
* * *
3278356 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGTCACGTAGTTGTGGACTTAAAAAGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
** * *
3278421 AGTTGTGGACTTTAAAAGGGTGCCATAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGA
66 AGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGA
3278486 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
129 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* * * * *
3278520 GGGTGCCACAGAGTTGTGGACTTAAAAAGATGTCACAGAGTTGTGGACTTTAAAAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
3278576 AAAATGCCAC
Statistics
Matches: 654, Mismatches: 50, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
162 76 0.12
163 141 0.22
164 355 0.54
165 82 0.13
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (162 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
TAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:3278576 original size:27 final size:27
Alignment explanation
Indices: 3277701--3278575 Score: 1345
Period size: 27 Copynumber: 32.0 Consensus size: 27
3277691 GCTTTGAAAT
* *
3277701 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3277728 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
* * **
3277756 GGGTGCCATGAAGTTGTGGTTTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3277783 GGGATGCCACAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
3277811 GGGTGCCATGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3277838 GGGTGCCACGGAGTTGTGGACTTAATA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3277865 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3277892 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3277919 GGGTACCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3277946 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3277973 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
3278000 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3278027 GGGATGCCATGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
**
3278055 GGGTGCCACGGAGTTGTGGTTTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
3278082 GGGATGCCATAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
3278110 GGGTGCCATGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3278137 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3278164 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3278191 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3278218 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
3278246 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
3278274 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
3278301 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3278328 GGGATGCCACGGAGTTGTAGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
3278356 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
3278383 GGGTGTCACGTAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3278410 AGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
**
3278438 GGGTGCCATAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
3278465 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
3278493 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3278520 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * * *
3278547 AGATGTCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
3278575 G
1 G
3278576 AAAATGCCAC
Statistics
Matches: 777, Mismatches: 61, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
27 553 0.71
28 224 0.29
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:3285849 original size:23 final size:23
Alignment explanation
Indices: 3285801--3285850 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
3285791 TATTTTTTAT
* * *
3285801 TTTTTTAAAACAAATAAAGATCA
1 TTTTTTAAAACAAAAAAACATAA
3285824 TTTTTTAAAA-AAAAAAACATAA
1 TTTTTTAAAACAAAAAAACATAA
*
3285846 ATTTT
1 TTTTT
3285851 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
TTTTTTAAAACAAAAAAACATAA
Found at i:3293127 original size:21 final size:21
Alignment explanation
Indices: 3293087--3293127 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3293077 TGGATATGTT
*
3293087 AAAATGCATGGAACATGGCTC
1 AAAATGCATGAAACATGGCTC
3293108 AAAATGCAT-AAACATAGGCT
1 AAAATGCATGAAACAT-GGCT
3293128 GTTTAGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
AAAATGCATGAAACATGGCTC
Found at i:3294136 original size:20 final size:20
Alignment explanation
Indices: 3294064--3294137 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
3294054 CAAAATCCAC
* *
3294064 AATGTATCGATACAATGAGA
1 AATGTATCGATACATTGAAA
***
3294084 AATGTATCGATACAATT-TCT
1 AATGTATCGATAC-ATTGAAA
* * *
3294104 TATGTGTCAATACATTGAAA
1 AATGTATCGATACATTGAAA
3294124 AATGTATCGATACA
1 AATGTATCGATACA
3294138 AATTCCTTCT
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
19 3 0.08
20 34 0.87
21 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:3296804 original size:69 final size:68
Alignment explanation
Indices: 3296665--3296834 Score: 173
Period size: 69 Copynumber: 2.5 Consensus size: 68
3296655 ACCTCGGTAG
* * * **
3296665 TACATTCAGTGATACCAAGTTACTTCCATCAAGTAAAGACTTAATAAAGTCTTATTGCCATTTTG
1 TACATTCAGTGAAACCAAGTCACTTCCATCAAATAAAGACTTAATAAAGTCTTATCACCA-TTTG
*
3296730 GCAT
65 ACAT
* * *
3296734 TACATTCAATGAAACCAAGTCATTTCCATCAAATAAAGACTTCATAAAGTCTGATCATCACCA-T
1 TACATTCAGTGAAACCAAGTCACTTCCATCAAATAAAGACTTAATAAAGTCT--T-ATCACCATT
3296798 T-ACAT
63 TGACAT
* * * *
3296803 TATATTTAGTGACACCAAGTCACTCCCATCAA
1 TACATTCAGTGAAACCAAGTCACTTCCATCAA
3296835 GACTAAACTT
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
69 75 0.90
70 2 0.02
71 1 0.01
72 5 0.06
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (68 bp):
TACATTCAGTGAAACCAAGTCACTTCCATCAAATAAAGACTTAATAAAGTCTTATCACCATTTGA
CAT
Found at i:3300295 original size:18 final size:18
Alignment explanation
Indices: 3300268--3300308 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3300258 TTTCAAACAT
*
3300268 CACTAGCAGACAAAAAGA
1 CACTAACAGACAAAAAGA
* *
3300286 CACTAACAGACATAAAGG
1 CACTAACAGACAAAAAGA
3300304 CACTA
1 CACTA
3300309 CCACTTCACA
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:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (18 bp):
CACTAACAGACAAAAAGA
Found at i:3301423 original size:2 final size:2
Alignment explanation
Indices: 3301416--3301451 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3301406 CATATGTATG
3301416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3301452 CACGTAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3306057 original size:2 final size:2
Alignment explanation
Indices: 3306050--3306087 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3306040 GTCTCGGTAC
3306050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3306088 GTTATAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3308800 original size:21 final size:21
Alignment explanation
Indices: 3308756--3308800 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3308746 TTAATTATTT
**
3308756 ATTAAGACTTTTTCCAATGTA
1 ATTAAGACTTTTTCCAATCAA
* *
3308777 ATTAAGATTTTTTCTAATCAA
1 ATTAAGACTTTTTCCAATCAA
3308798 ATT
1 ATT
3308801 TTTTATTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (21 bp):
ATTAAGACTTTTTCCAATCAA
Found at i:3310266 original size:79 final size:78
Alignment explanation
Indices: 3310183--3310748 Score: 573
Period size: 79 Copynumber: 7.2 Consensus size: 78
3310173 AAATTTAATA
* * * ** * *
3310183 TTTTGGAGATAAAAACGGGATTGGAGTATCCTCTCGAAAATAATAGGGTTAGAGTATCCCCGATG
1 TTTTGGAAATAAAATCGGG-TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
*
3310248 GTGAAAAATCAATG
65 GTGAAAAATCGATG
* * * * *
3310262 TTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTTGAAAATAA-TGGGTTAGAGTATTCCCGATT
1 TTTTGGAAATAAAATC-GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
* *
3310326 GTGAAAAATTGATA
65 GTGAAAAATCGATG
* * ** * *
3310340 TCTTAGAAATAAAGCCGAAGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
1 TTTTGGAAATAAAATCG-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
*
3310405 ATGAAAAATC-AGTG
65 GTGAAAAATCGA-TG
* * *
3310419 TTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCAATT
1 TTTTGGAAATAAAATCG-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
* *
3310484 GTGAAAAATTTG-TA
65 GTGAAAAA-TCGATG
* * * * *
3310498 TTTTAGAAATAAAATTGGGGTTGGAATATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTGATT
1 TTTTGGAAATAAAA-TCGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
* *
3310563 ATGGAAAATCGATG
65 GTGAAAAATCGATG
* * * * *
3310577 TTTTGGAAATAAAACCGAGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGAAGTATTCCCGA-T
1 TTTTGGAAATAAAATCG-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
* *
3310641 GATGAAAAATTGGTG
65 G-TGAAAAATCGATG
* * * * *
3310656 TTTTAGAAATAAAATCGAGGTTGGAGTATCCCTTCGGAAACAACGGGGTTGGAGTATCCCCGATG
1 TTTTGGAAATAAAATCG-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATT
* *
3310721 GTGAAAAATCGGTA
65 GTGAAAAATCGATG
*
3310735 TTTTAGAAATAAAA
1 TTTTGGAAATAAAA
3310749 ACATGAATGA
Statistics
Matches: 408, Mismatches: 68, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
77 1 0.00
78 69 0.17
79 331 0.81
80 7 0.02
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (78 bp):
TTTTGGAAATAAAATCGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTG
TGAAAAATCGATG
Found at i:3310555 original size:158 final size:158
Alignment explanation
Indices: 3310172--3310748 Score: 687
Period size: 158 Copynumber: 3.7 Consensus size: 158
3310162 TCCCTCGATG
* * * * * ** *
3310172 AAAATTTAATATTTTGGAGATAAAAACG-GGATTGGAGTATCCTCTCGAAAATAATAGGGTTAGA
1 AAAATTT-GTATTTTAGAAATAAAATCGAGG-TTGGAGTATCCCCTCGAAAATAACGGGGTTGGA
* * * *
3310236 GTATCCCCGATGGTGAAAAATCAATGTTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTTGAAA
64 GTATCCCCGATGATGAAAAATCAGTGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAA
*
3310301 ATAAT-GGGTTAGAGTATTCCCGATTGTGA
129 ATAATGGGGTTGGAGTATTCCCGATTGTGA
* ** * *
3310330 AAAA-TTGATATCTTAGAAATAAAGCCGAAGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAG
1 AAAATTTG-TATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAG
* * *
3310394 TATCCCCGATTATGAAAAATCAGTGTTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCAAAAA
65 TATCCCCGATGATGAAAAATCAGTGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAA
* *
3310459 TAATGGGGTTGGAGTATCCCCAATTGTGA
130 TAATGGGGTTGGAGTATTCCCGATTGTGA
* * * *
3310488 AAAATTTGTATTTTAGAAATAAAATTGGGGTTGGAATATCCCCTCAAAAATAACGGGGTTGGAGT
1 AAAATTTGTATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
* * * *
3310553 ATCCCTGATTATGGAAAATC-GATGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCTTCGAAAA
66 ATCCCCGATGATGAAAAATCAG-TGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAA
* * *
3310617 TAACGAGGTTGAAGTATTCCCGA-TGATGA
130 TAATGGGGTTGGAGTATTCCCGATTG-TGA
* * * * *
3310646 AAAATTGGTGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCTTCGGAAACAACGGGGTTGGAGT
1 AAAATTTGTATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
* * * *
3310711 ATCCCCGATGGTGAAAAATCGGTATTTTAGAAATAAAA
66 ATCCCCGATGATGAAAAATCAGTGTTTTGGAAATAAAA
3310749 ACATGAATGA
Statistics
Matches: 356, Mismatches: 56, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
157 110 0.31
158 242 0.68
159 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (158 bp):
AAAATTTGTATTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT
ATCCCCGATGATGAAAAATCAGTGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAAT
AATGGGGTTGGAGTATTCCCGATTGTGA
Found at i:3310685 original size:237 final size:236
Alignment explanation
Indices: 3310203--3310748 Score: 707
Period size: 237 Copynumber: 2.3 Consensus size: 236
3310193 AAAAACGGGA
* * * * * *
3310203 TTGGAGTATCCTCTCGAAAATAATAGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTGG
1 TTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTATTTTAG
* ** * *
3310268 AAATAAAACCGGGGTTGGAGTATCCCCTTGAAAATAATGGGTTAGAGTATTCCCGATTGTGAAAA
66 AAATAAAACCGGGGTTGGAATATCCCCTCAAAAATAAGGGGTTAGAGTATTCCCGATTATGAAAA
* * * *
3310333 ATTGATATCTTAGAAATAAAGCCGAAGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATC
131 ATCGATATCTTAGAAATAAAACCGAAGTTAGAGTATCCCCTCGAAAATAACGAGGTTGAAGTATC
* *
3310398 CCCGATTATGAAAAATCAGTGTTTTGGAAATAAAATCGAGG
196 CCCGATGATGAAAAATCAGTGTTTTAGAAATAAAATCGAGG
* * * **
3310439 TTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCAATTGTGAAAAATTTGTATTTTAG
1 TTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTATTTTAG
** * *
3310504 AAATAAAATTGGGGTTGGAATATCCCCTCAAAAATAACGGGGTTGGAGTA-TCCCTGATTATGGA
66 AAATAAAACCGGGGTTGGAATATCCCCTCAAAAATAA-GGGGTTAGAGTATTCCC-GATTATGAA
* * * * * *
3310568 AAATCGATGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGAAGTA
129 AAATCGATATCTTAGAAATAAAACCGAAGTTAGAGTATCCCCTCGAAAATAACGAGGTTGAAGTA
* **
3310633 TTCCCGATGATGAAAAATTGGTGTTTTAGAAATAAAATCGAGG
194 TCCCCGATGATGAAAAATCAGTGTTTTAGAAATAAAATCGAGG
* * * * *
3310676 TTGGAGTATCCCTTCGGAAACAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGGTATTTTAG
1 TTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTATTTTAG
3310741 AAATAAAA
66 AAATAAAA
3310749 ACATGAATGA
Statistics
Matches: 264, Mismatches: 44, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
236 90 0.34
237 174 0.66
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (236 bp):
TTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTATTTTAG
AAATAAAACCGGGGTTGGAATATCCCCTCAAAAATAAGGGGTTAGAGTATTCCCGATTATGAAAA
ATCGATATCTTAGAAATAAAACCGAAGTTAGAGTATCCCCTCGAAAATAACGAGGTTGAAGTATC
CCCGATGATGAAAAATCAGTGTTTTAGAAATAAAATCGAGG
Found at i:3313159 original size:30 final size:30
Alignment explanation
Indices: 3313107--3313178 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
3313097 TACATTGAGC
* * * *
3313107 AATGAATCAATACATTTGGGTAAAACCCAA
1 AATGTATCGATACATATAGGTAAAACCCAA
3313137 AATGTATCGATACATATAGGTAAAACCCAA
1 AATGTATCGATACATATAGGTAAAACCCAA
3313167 AATGTATCGATA
1 AATGTATCGATA
3313179 TAATGAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (30 bp):
AATGTATCGATACATATAGGTAAAACCCAA
Found at i:3313551 original size:44 final size:43
Alignment explanation
Indices: 3313486--3313915 Score: 220
Period size: 44 Copynumber: 10.2 Consensus size: 43
3313476 AGCCCGAACA
* * *
3313486 AAATGAGGTGCACCCTACTCTTTGAAGACAAAGGGAAAAAAAGG
1 AAATGAGGTGCATCCTGCTCTTTGAGGACAAA-GGAAAAAAAGG
3313530 AAATGAGGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAGAA--
1 AAATGAGGTGCATCCTGCTCTTTGAGGACAAAGGAAAAA-AAGG
* * * * *
3313572 AAA-AAAGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAA-A
1 AAATGAGGTGCATCCTGCTCTTTGAGGAC-AAA-GGAAAA-AAAGG
** *** * * * *
3313616 AAATGAAATATGTCCTACTCTTTAAGGACAAAAG-AGAAAAGG
1 AAATGAGGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAAAGG
* * *
3313658 AAA--A-G-GCATCCTACTTTTTGAGGACAAAGG-AAAAAAGA
1 AAATGAGGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAAAGG
* * * *
3313696 AAATAAAAAGTGTGC--CTTTCTCTTTGAGGACAAAAGGGAAAAGAAGG
1 AAAT---GAG-GTGCATCCTGCTCTTTGAGGAC-AAA-GGAAAAAAAGG
** ** * * * *
3313743 AAATGAAATGTGTCATGCTCTTT-AAGACAAAAG-AGAAAAGG
1 AAATGAGGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAAAGG
* * *
3313784 AAA--A-G-GCATCCTGCACTTTGAGGACTAAGGGAAAAGAAGG
1 AAATGAGGTGCATCCTGCTCTTTGAGGAC-AAAGGAAAAAAAGG
*
3313824 AAATGAGGTGCA-CCTTGGTCTTTGAGGACAAAGG--AAAAAGG
1 AAATGAGGTGCATCC-TGCTCTTTGAGGACAAAGGAAAAAAAGG
* * * *
3313865 AAATAAAGTGCATCTTGCTCTTTGAGAACAAAGGGAAAAAAA-G
1 AAATGAGGTGCATCCTGCTCTTTGAGGACAAA-GGAAAAAAAGG
3313908 AAATGAGG
1 AAATGAGG
3313916 AAAATGTCCT
Statistics
Matches: 294, Mismatches: 60, Indels: 65
0.70 0.14 0.16
Matches are distributed among these distances:
37 10 0.03
38 32 0.11
39 4 0.01
40 10 0.03
41 64 0.22
42 16 0.05
43 36 0.12
44 76 0.26
45 32 0.11
46 4 0.01
47 10 0.03
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.19
Consensus pattern (43 bp):
AAATGAGGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAAAGG
Done.