Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold312
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: 1822960
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 12
Found at i:470738 original size:72 final size:71
Alignment explanation
Indices: 470616--470803 Score: 288
Period size: 72 Copynumber: 2.6 Consensus size: 71
470606 AAAAGTCACA
470616 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATATATGAATGTATAAATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATATATGAATGTATAAATACAT
470681 TCTGTCC
66 TCTGT-C
** * *
470688 TTTTTACCCAGATGTATCGATACATTTTTTGATGTAAT-GATACATGTATGAATGTATTAATACA
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGT-ATCGATACATATATGAATGTATAAATACA
470752 TTCTGTC
65 TTCTGTC
* * *
470759 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
470804 TCTATCTTTT
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
70 2 0.02
71 39 0.37
72 63 0.59
73 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATATATGAATGTATAAATACAT
TCTGTC
Found at i:470781 original size:51 final size:51
Alignment explanation
Indices: 470718--470853 Score: 220
Period size: 51 Copynumber: 2.7 Consensus size: 51
470708 TACATTTTTT
* *
470718 GATGTAAT-GATACATGTATGAATGTATTAATACATTCTGTCTTTTTACCCA
1 GATGT-ATCGATACATGTATGAATGTATCAATACATTCTATCTTTTTACCCA
*
470769 GATGTATCGATACATGTATGAATGTATCGATACATTCTATCTTTTTACCCA
1 GATGTATCGATACATGTATGAATGTATCAATACATTCTATCTTTTTACCCA
*
470820 GATGTATCGATACATGTATGAATGTATCGATACA
1 GATGTATCGATACATGTATGAATGTATCAATACA
470854 AGTATGAATG
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
50 2 0.02
51 79 0.98
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (51 bp):
GATGTATCGATACATGTATGAATGTATCAATACATTCTATCTTTTTACCCA
Found at i:470828 original size:31 final size:31
Alignment explanation
Indices: 470790--470933 Score: 135
Period size: 31 Copynumber: 4.4 Consensus size: 31
470780 ACATGTATGA
470790 ATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACATTCTATCTTTTTACCCAG
* * ** **
470821 ATGTATCGATACATGTATGAATGTATCGATACAAGTATG
1 ATGTATCGATACAT-TCT--ATCT-T-TTTAC--CCA-G
* *
470860 AATGTATCGATACATTTTGTCTTTTTACCCAG
1 -ATGTATCGATACATTCTATCTTTTTACCCAG
470892 ATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACATTCTATCTTTTTACCCAG
470923 ATGTATCGATA
1 ATGTATCGATA
470934 TATTGAATAA
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
31 54 0.61
32 3 0.03
33 1 0.01
34 3 0.03
35 4 0.04
36 4 0.04
37 2 0.02
38 1 0.01
39 3 0.03
40 14 0.16
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (31 bp):
ATGTATCGATACATTCTATCTTTTTACCCAG
Found at i:470845 original size:71 final size:71
Alignment explanation
Indices: 470770--470905 Score: 245
Period size: 71 Copynumber: 1.9 Consensus size: 71
470760 TTTTACCCAG
*
470770 ATGTATCGATACATGTATGAATGTATCGATACATTCTATCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACAAGTATGAATGTATCGATACATTCTATCTTTTTACCCAGATGTATCGATACAT
470835 GTATGA
66 GTATGA
* *
470841 ATGTATCGATACAAGTATGAATGTATCGATACATTTTGTCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACAAGTATGAATGTATCGATACATTCTATCTTTTTACCCAGATGTATCGATACAT
470906 TCTATCTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (71 bp):
ATGTATCGATACAAGTATGAATGTATCGATACATTCTATCTTTTTACCCAGATGTATCGATACAT
GTATGA
Found at i:470846 original size:20 final size:20
Alignment explanation
Indices: 470821--470874 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
470811 TTTTACCCAG
470821 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATGA
*
470841 ATGTATCGATACAAGTATGA
1 ATGTATCGATACATGTATGA
470861 ATGTATCGATACAT
1 ATGTATCGATACAT
470875 TTTGTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATGTATGA
Found at i:470865 original size:122 final size:123
Alignment explanation
Indices: 470647--470905 Score: 389
Period size: 122 Copynumber: 2.1 Consensus size: 123
470637 ACATTTTTCA
*
470647 ATGTATCGATACATATATGAATGTATAAATACATTCTGTCCTTTTTACCCAGATGTATCGATACA
1 ATGTATCGATACATATATGAATGTATAAATACATTCTATCCTTTTTACCCAGATGTATCGATACA
* * * *
470712 TTTTTTGATGTAATGATACATGTATGAATGTATTAATACATTCTGTCTTTTTACCCAG
66 TTGTATGATGTAATGATACAAGTATGAATGTATCAATACATTCTGTCTTTTTACCCAG
* **
470770 ATGTATCGATACATGTATGAATGTATCGATACATTCTAT-CTTTTTACCCAGATGTATCGATACA
1 ATGTATCGATACATATATGAATGTATAAATACATTCTATCCTTTTTACCCAGATGTATCGATACA
* *
470834 -TGTATGAATGT-ATCGATACAAGTATGAATGTATCGATACATTTTGTCTTTTTACCCAG
66 TTGTATG-ATGTAAT-GATACAAGTATGAATGTATCAATACATTCTGTCTTTTTACCCAG
470892 ATGTATCGATACAT
1 ATGTATCGATACAT
470906 TCTATCTTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
121 6 0.05
122 83 0.67
123 35 0.28
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (123 bp):
ATGTATCGATACATATATGAATGTATAAATACATTCTATCCTTTTTACCCAGATGTATCGATACA
TTGTATGATGTAATGATACAAGTATGAATGTATCAATACATTCTGTCTTTTTACCCAG
Found at i:475230 original size:16 final size:16
Alignment explanation
Indices: 475200--475299 Score: 92
Period size: 16 Copynumber: 6.2 Consensus size: 16
475190 TTTTGGGTTG
*
475200 TTTTCGGGTTTGGGTCA
1 TTTT-GGGTTCGGGTCA
475217 TTTTGGGTTCGGGTCA
1 TTTTGGGTTCGGGTCA
*
475233 TTTCGGGTTCGGGTCA
1 TTTTGGGTTCGGGTCA
* *
475249 CTTTGGATTCGGGTCA
1 TTTTGGGTTCGGGTCA
* * * **
475265 TTTCGAGTTCGAGTTG
1 TTTTGGGTTCGGGTCA
* *
475281 TTTTGGATTCGAGTCA
1 TTTTGGGTTCGGGTCA
475297 TTT
1 TTT
475300 CAAGTTCGGG
Statistics
Matches: 66, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
16 62 0.94
17 4 0.06
ACGTcount: A:0.10, C:0.14, G:0.32, T:0.44
Consensus pattern (16 bp):
TTTTGGGTTCGGGTCA
Found at i:475237 original size:32 final size:32
Alignment explanation
Indices: 475201--475312 Score: 125
Period size: 32 Copynumber: 3.5 Consensus size: 32
475191 TTTGGGTTGT
* * *
475201 TTTCGGGTTTGGGTCATTTTGGGTTCGGGTCA
1 TTTCGGGTTCGGGTCACTTTGGATTCGGGTCA
475233 TTTCGGGTTCGGGTCACTTTGGATTCGGGTCA
1 TTTCGGGTTCGGGTCACTTTGGATTCGGGTCA
* * *** *
475265 TTTCGAGTTCGAGTTGTTTTGGATTCGAGTCA
1 TTTCGGGTTCGGGTCACTTTGGATTCGGGTCA
**
475297 TTTCAAGTTCGGGTCA
1 TTTCGGGTTCGGGTCA
475313 ATCGGGTTTA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.12, C:0.15, G:0.32, T:0.41
Consensus pattern (32 bp):
TTTCGGGTTCGGGTCACTTTGGATTCGGGTCA
Found at i:476382 original size:16 final size:16
Alignment explanation
Indices: 476361--476499 Score: 79
Period size: 16 Copynumber: 8.6 Consensus size: 16
476351 AATTATTCAG
476361 GTCATTTCAGGTTCGA
1 GTCATTTCAGGTTCGA
* * *
476377 GTCATTTCAGATTTGG
1 GTCATTTCAGGTTCGA
476393 GTCATTTC-GAGTTCGA
1 GTCATTTCAG-GTTCGA
*
476409 GTCATTT-TGGATTC-A
1 GTCATTTCAGG-TTCGA
* *
476424 GGTCATTTTAAGGTTCAA
1 -GTCA-TTTCAGGTTCGA
* *
476442 GTCA-TTCTGGATTCGG
1 GTCATTTCAGG-TTCGA
* * **
476458 GTCATTTTAGATTTAA
1 GTCATTTCAGGTTCGA
*
476474 GTCATTTCGGGTTCGA
1 GTCATTTCAGGTTCGA
*
476490 GTCAGTTCAG
1 GTCATTTCAG
476500 ATTCAGGTTG
Statistics
Matches: 90, Mismatches: 24, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
15 7 0.08
16 67 0.74
17 13 0.14
18 3 0.03
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.40
Consensus pattern (16 bp):
GTCATTTCAGGTTCGA
Found at i:476398 original size:32 final size:32
Alignment explanation
Indices: 476355--476499 Score: 123
Period size: 32 Copynumber: 4.5 Consensus size: 32
476345 CGAGTTAATT
* *
476355 ATTCAGGTCATTTCAGGTTCGAGTCATTTCAG
1 ATTCGGGTCATTTCAGGTTCGAGTCATTTCGG
* *
476387 ATTTGGGTCATTTC-GAGTTCGAGTCATTTTGG
1 ATTCGGGTCATTTCAG-GTTCGAGTCATTTCGG
* * *
476419 ATTCAGGTCATTTTAAGGTTCAAGTCA-TTCTGG
1 ATTCGGGTCA-TTTCAGGTTCGAGTCATTTC-GG
* * **
476452 ATTCGGGTCATTTTAGATTTAAGTCATTTCGG
1 ATTCGGGTCATTTCAGGTTCGAGTCATTTCGG
* * *
476484 GTTCGAGTCAGTTCAG
1 ATTCGGGTCATTTCAG
476500 ATTCAGGTTG
Statistics
Matches: 91, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
31 1 0.01
32 63 0.69
33 26 0.29
34 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (32 bp):
ATTCGGGTCATTTCAGGTTCGAGTCATTTCGG
Found at i:476477 original size:65 final size:64
Alignment explanation
Indices: 476355--476480 Score: 148
Period size: 65 Copynumber: 2.0 Consensus size: 64
476345 CGAGTTAATT
* * * * *
476355 ATTCAGGTCATTTCAGGTTCGAGTCATTTCAGATTTGGGTCATTTCGAGTTCGAGTCATTTTGG
1 ATTCAGGTCATTTAAGGTTCAAGTCATTTCAGATTCGGGTCATTTAGAGTTCAAGTCATTTTGG
* *
476419 ATTCAGGTCATTTTAAGGTTCAAGTCA-TTCTGGATTCGGGTCATTTTAGA-TTTAAGTCATTT
1 ATTCAGGTCA-TTTAAGGTTCAAGTCATTTC-AGATTCGGGTCA-TTTAGAGTTCAAGTCATTT
476481 CGGGTTCGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
64 13 0.25
65 34 0.65
66 5 0.10
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.42
Consensus pattern (64 bp):
ATTCAGGTCATTTAAGGTTCAAGTCATTTCAGATTCGGGTCATTTAGAGTTCAAGTCATTTTGG
Found at i:476677 original size:21 final size:22
Alignment explanation
Indices: 476641--476682 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
476631 AAAGGTCAGA
476641 ACCCTAGAAAGTATCGATACAC
1 ACCCTAGAAAGTATCGATACAC
*
476663 ACCCTAG-ATGTATCGATACA
1 ACCCTAGAAAGTATCGATACA
476683 TATTGCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (22 bp):
ACCCTAGAAAGTATCGATACAC
Found at i:476715 original size:33 final size:32
Alignment explanation
Indices: 476671--476735 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
476661 ACACCCTAGA
* *
476671 TGTATCGATACATATTGCTTAGTATTGATACAT
1 TGTATCAATACATATT-CTTAGTATCGATACAT
* *
476704 TGTATCAATACATGTTCTTGGTATCGATACAT
1 TGTATCAATACATATTCTTAGTATCGATACAT
476736 CATGAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (32 bp):
TGTATCAATACATATTCTTAGTATCGATACAT
Found at i:476812 original size:10 final size:10
Alignment explanation
Indices: 476793--476849 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 10
476783 TTAATTGATA
476793 CATCACTGTT
1 CATCACTGTT
*
476803 CATCATTGTT
1 CATCACTGTT
476813 CATCACTGTT
1 CATCACTGTT
476823 --T-A-TG-T
1 CATCACTGTT
*
476828 -ATCACTATT
1 CATCACTGTT
476837 CATCACTGTT
1 CATCACTGTT
476847 CAT
1 CAT
476850 GTATCGATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
5 1 0.03
6 3 0.08
7 2 0.05
8 2 0.05
9 1 0.03
10 29 0.76
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.44
Consensus pattern (10 bp):
CATCACTGTT
Found at i:478951 original size:21 final size:21
Alignment explanation
Indices: 478927--478978 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
478917 GAACTACAGG
*
478927 AGAAAATGAATAAGTTGGAAA
1 AGAAAATGAATAAGTTGAAAA
*
478948 AGAAAA-GAAATGAGTTGAAAA
1 AGAAAATG-AATAAGTTGAAAA
478969 ATGAAAATGA
1 A-GAAAATGA
478979 TGAGTTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 18 0.69
22 6 0.23
23 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (21 bp):
AGAAAATGAATAAGTTGAAAA
Found at i:479636 original size:17 final size:18
Alignment explanation
Indices: 479607--479643 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
479597 ATATGAGAAA
479607 TTGTTGAAAATTTGT-TT
1 TTGTTGAAAATTTGTGTT
479624 TTGTT-AAACATTTGTGTT
1 TTGTTGAAA-ATTTGTGTT
479642 TT
1 TT
479644 TGTGTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 11 0.61
18 4 0.22
ACGTcount: A:0.22, C:0.03, G:0.16, T:0.59
Consensus pattern (18 bp):
TTGTTGAAAATTTGTGTT
Found at i:481409 original size:30 final size:31
Alignment explanation
Indices: 481370--481429 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
481360 GGTGAGAATG
* * *
481370 TATTTAGGGGGCGAGTTTACATAAA-ATTTT
1 TATTAAGGGGGAGAGCTTACATAAACATTTT
*
481400 TATTAAGGGGGAGAGCTTGCATAAACATTT
1 TATTAAGGGGGAGAGCTTACATAAACATTT
481430 GGTATTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (31 bp):
TATTAAGGGGGAGAGCTTACATAAACATTTT
Found at i:481634 original size:96 final size:96
Alignment explanation
Indices: 481470--481662 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
481460 GAAAATAGAT
*
481470 TTTCTTTATAACAAAAAGGGGAGAATTCACTAAAAGTTTACAAATAAGGGGAGAGTTCATGAAAG
1 TTTCTTTATAACAAAAAGGGGAGAATTCACTAAAAGTTTAAAAATAAGGGGAGAGTTCATGAAAG
481535 AAATATTTCAGGTTATAAAAGTTAAAATTCG
66 AAATATTTCAGGTTATAAAAGTTAAAATTCG
481566 TTTCTTTATAACAAAAAGGGGAGAATTCACTAAAAGTTTAAAAATAAGGGGAGAGTTCATGAAAG
1 TTTCTTTATAACAAAAAGGGGAGAATTCACTAAAAGTTTAAAAATAAGGGGAGAGTTCATGAAAG
*
481631 AAATATTTCGGGTTATAAAAGTTAAAATTCG
66 AAATATTTCAGGTTATAAAAGTTAAAATTCG
481662 T
1 T
481663 ATTAAGAAAC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.30
Consensus pattern (96 bp):
TTTCTTTATAACAAAAAGGGGAGAATTCACTAAAAGTTTAAAAATAAGGGGAGAGTTCATGAAAG
AAATATTTCAGGTTATAAAAGTTAAAATTCG
Found at i:482240 original size:13 final size:13
Alignment explanation
Indices: 482222--482246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
482212 ATATTGCTTA
482222 GTATCGATACATT
1 GTATCGATACATT
482235 GTATCGATACAT
1 GTATCGATACAT
482247 AGTTCTTCGT
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):
GTATCGATACATT
Found at i:482370 original size:24 final size:24
Alignment explanation
Indices: 482335--482399 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
482325 CATTACTGTA
*
482335 CATCACTATTCATGTATCACTAGT
1 CATCACTGTTCATGTATCACTAGT
* *
482359 CATCACTGTTCATGCATCACTATT
1 CATCACTGTTCATGTATCACTAGT
*
482383 CATCACCGTTCATGTAT
1 CATCACTGTTCATGTAT
482400 TGATACATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (24 bp):
CATCACTGTTCATGTATCACTAGT
Found at i:482915 original size:36 final size:34
Alignment explanation
Indices: 482867--482959 Score: 120
Period size: 36 Copynumber: 2.8 Consensus size: 34
482857 CTAAATGATT
*
482867 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGG
1 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAAG
*
482901 GAAAGAGGTTCTATCTTAGCCTGTG-AAAAGATAAG
1 G--AGAGGTTCTATCTTAGCCTTTGAAAAAGATAAG
*
482936 GAG-GTTTCTATCTTAGCC-TTGAAA
1 GAGAGGTTCTATCTTAGCCTTTGAAA
482960 GATAGTGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
31 2 0.04
32 16 0.31
33 2 0.04
34 1 0.02
35 10 0.19
36 21 0.40
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (34 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAAG
Found at i:486017 original size:19 final size:20
Alignment explanation
Indices: 485974--486020 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
485964 AAATCAGTTT
*
485974 TAAAATTTTTCTTTTATTTCA
1 TAAAA-TTTTCATTTATTTCA
*
485995 TAAAATTTTCATTT-TTTCC
1 TAAAATTTTCATTTATTTCA
486014 TAAAATT
1 TAAAATT
486021 CTCCTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 8 0.33
21 5 0.21
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (20 bp):
TAAAATTTTCATTTATTTCA
Found at i:486351 original size:143 final size:143
Alignment explanation
Indices: 486091--486356 Score: 371
Period size: 143 Copynumber: 1.9 Consensus size: 143
486081 GCTTAAAAAG
* *
486091 TTTAAAATTCATCAAATATTATCATTTAATTCACATTAAATCAGTTTTGAAAATTTCCTTTTCTT
1 TTTAAAATTCATCAAATATCATCATTTAATTCACATTAAATCAGTTTTGAAAATTTCATTTTCTT
* * *
486156 TCATGAATTTTTTATTTTTTCTTAAAATTTTTCTATTTTCAAAATACGGAGTTTTCTACTCCGTA
66 TCATGAATTTTTCACTTTTTCTTAAAATTTTTCTATTTTAAAAATACGGAGTTTTCTACTCCGTA
486221 AATGCTTTTGAGT
131 AATGCTTTTGAGT
* *
486234 TTTAAAATTCATCAAATATCATCATTTAATTCATATTAAATCATTTTTGAAAA-TTCATTTAT-T
1 TTTAAAATTCATCAAATATCATCATTTAATTCACATTAAATCAGTTTTGAAAATTTCATTT-TCT
* *
486297 TTCAT-AAGTTTTTCACTTTTTCTTTGAAATTTTTTTATTTTTGAAAAAT-C-GAGTTTTCTA
65 TTCATGAA-TTTTTCACTTTTTC-TTAAAATTTTTCTA-TTTT-AAAAATACGGAGTTTTCTA
486357 TTCCAAAAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
141 2 0.02
142 24 0.22
143 73 0.67
144 5 0.05
145 5 0.05
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (143 bp):
TTTAAAATTCATCAAATATCATCATTTAATTCACATTAAATCAGTTTTGAAAATTTCATTTTCTT
TCATGAATTTTTCACTTTTTCTTAAAATTTTTCTATTTTAAAAATACGGAGTTTTCTACTCCGTA
AATGCTTTTGAGT
Found at i:488506 original size:150 final size:148
Alignment explanation
Indices: 488326--489000 Score: 701
Period size: 150 Copynumber: 4.6 Consensus size: 148
488316 GCACCCCCAA
* * * *
488326 GGTATTTTCATAATTTTTTA-AAACTGAGCCCTAATTTGTCATTAGGTCGCTTCTATGCCAAGAG
1 GGTATTTTCATAATTTTTTAGAAACTGAGTCCTAATTTGTCA-CAGGTCACTTCTATGCCAAGGG
*
488390 TACGTATTAGGCATAGGTTCACTTTTTTCTTTTTAAGTCTTTTAGGGTTATC-GAAATACTTTCA
65 TACGTATTAGGCATAGGTTCAC-TTTTTCTTTTTAAGTCCTTTAGGGTTA-CAGAAATACTTTCA
*
488454 TGTCGAAGGTGTACCCATAAG
128 TGTCGAAGGTATACCCATAAG
** * * * * **
488475 GGTATTTTTGTAATCTTTTTAGAATC-GAGCCCTAATTTATCACCAGATCGTTTCTATGCCAAGG
1 GGTATTTTCATAAT-TTTTTAGAAACTGAGTCCTAATTTGTCA-CAGGTCACTTCTATGCCAAGG
* * * * *
488539 GTATGTATTAGGCGTAGGTTCACTTTTCCTTTTTAAGTCCTTTAAGGTTACAAAAATACTTTCAT
64 GTACGTATTAGGCATAGGTTCACTTTTTCTTTTTAAGTCCTTTAGGGTTACAGAAATACTTTCAT
* *
488604 GTCGAACAGTATACCCGTAAG
129 GTCGAA-GGTATACCCATAAG
* * * * * *
488625 GGCATTTTCATAATTTTTTTAGAATC-GAGTCCTAATTTATCACCGAATCATTTCTATGCCAAGG
1 GGTATTTTCATAA-TTTTTTAGAAACTGAGTCCTAATTTGTCACAG-GTCACTTCTATGCCAAGG
* * *
488689 GTATGTATTAGGCATAGGTTCACTTTTTCTTTTTAAGTCCTTTAGGGTTACTG-GATACTTTCAT
64 GTACGTATTAGGCATAGGTTCACTTTTTCTTTTTAAGTCCTTTAGGGTTACAGAAATACTTTCAT
* *
488753 GTCAAAGGTATACCCATAAA
129 GTCGAAGGTATACCCATAAG
* * * *
488773 GGTATTTTCGTAATTTTTCTA-AAACTGAATCCT-ATTTGTCACCGAGT--C--CTATGCCAATG
1 GGTATTTTCATAATTTTT-TAGAAACTGAGTCCTAATTTGTCACAG-GTCACTTCTATGCCAAGG
* * * * * * *
488832 GTACATATTAGACGTAGGTTCACTTTTCCTTTTTAAGTCCTTTAGTGTTACTAG-GATACTTTTA
64 GTACGTATTAGGCATAGGTTCACTTTTTCTTTTTAAGTCCTTTAGGGTTAC-AGAAATACTTTCA
*
488896 TGTCGAAGGTATACCCATAGG
128 TGTCGAAGGTATACCCATAAG
* ** * *
488917 GGTATTTTCATAATTTTTCTAG-AACTGAGTCTTAATTTGTCATTGGGTCACTTCTATACCGAGG
1 GGTATTTTCATAATTTTT-TAGAAACTGAGTCCTAATTTGTCA-CAGGTCACTTCTATGCCAAGG
488981 GTACGTATTAGGCATAGGTT
64 GTACGTATTAGGCATAGGTT
489001 TGGTTTTTTT
Statistics
Matches: 446, Mismatches: 64, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
143 55 0.12
144 57 0.13
145 10 0.02
146 1 0.00
147 21 0.05
148 31 0.07
149 96 0.22
150 171 0.38
151 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (148 bp):
GGTATTTTCATAATTTTTTAGAAACTGAGTCCTAATTTGTCACAGGTCACTTCTATGCCAAGGGT
ACGTATTAGGCATAGGTTCACTTTTTCTTTTTAAGTCCTTTAGGGTTACAGAAATACTTTCATGT
CGAAGGTATACCCATAAG
Found at i:498189 original size:13 final size:13
Alignment explanation
Indices: 498171--498210 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
498161 TACAAAACTT
498171 ATGTATCGATACA
1 ATGTATCGATACA
498184 ATGTATCGATACA
1 ATGTATCGATACA
*
498197 TTGTATCGATACA
1 ATGTATCGATACA
498210 A
1 A
498211 CACTTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:503936 original size:13 final size:13
Alignment explanation
Indices: 503918--503942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
503908 ACAATTCTTC
503918 ATGTATCGATACT
1 ATGTATCGATACT
503931 ATGTATCGATAC
1 ATGTATCGATAC
503943 ATTGTCCCAT
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):
ATGTATCGATACT
Found at i:504042 original size:19 final size:19
Alignment explanation
Indices: 503992--504047 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
503982 CTACTAGTTT
*
503992 CATGTATCGATACAATTGGG
1 CATGTATCGATACAA-TGAG
* *
504012 TATGTATTGATACAATGAG
1 CATGTATCGATACAATGAG
* *
504031 CATGTGTCGATAAAATG
1 CATGTATCGATACAATG
504048 TATCGATACT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:512727 original size:19 final size:19
Alignment explanation
Indices: 512682--512737 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
512672 CTGCAAGTTT
*
512682 CATGTATCGATACAATTGGG
1 CATGTATCGATACAA-TGAG
* *
512702 TATGTATCAATACAATGAG
1 CATGTATCGATACAATGAG
512721 CATGTATCGATACAATG
1 CATGTATCGATACAATG
512738 TATCGACACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:513368 original size:101 final size:101
Alignment explanation
Indices: 513193--513394 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
513183 GAAATAATCC
513193 CCCCAAGTAAGTTTATGGAACCTCCAATACATGGAGATCACCATGAACTTGGTGTTTTATTAACA
1 CCCCAAGTAAGTTTATGGAACCTCCAATACATGGAGATCACCATGAACTTGGTGTTTTATTAACA
513258 AGATCTTGATCTTGGGGGTACATTAAGCTTAAAGTT
66 AGATCTTGATCTTGGGGGTACATTAAGCTTAAAGTT
513294 CCCCAAGTAAGTTTATGGAACCTCCAATACATGGAGATCACCATGAACTTGGTGTTTTATTAACA
1 CCCCAAGTAAGTTTATGGAACCTCCAATACATGGAGATCACCATGAACTTGGTGTTTTATTAACA
513359 AGATCTTGATCTTGGGGGTACATTAAGCTTAAAGTT
66 AGATCTTGATCTTGGGGGTACATTAAGCTTAAAGTT
513395 TGGATTCATG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (101 bp):
CCCCAAGTAAGTTTATGGAACCTCCAATACATGGAGATCACCATGAACTTGGTGTTTTATTAACA
AGATCTTGATCTTGGGGGTACATTAAGCTTAAAGTT
Found at i:515605 original size:2 final size:2
Alignment explanation
Indices: 515598--515674 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
515588 CTTAGTCCTA
*
515598 AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
515640 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
515675 AAAGAGATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.48, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:517320 original size:20 final size:21
Alignment explanation
Indices: 517295--517334 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
517285 GATATACCCC
* *
517295 AAAATCTATATTTTA-AAAAA
1 AAAATCAAAATTTTACAAAAA
517315 AAAATCAAAATTTTACAAAA
1 AAAATCAAAATTTTACAAAA
517335 GATTGGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATCAAAATTTTACAAAAA
Found at i:519686 original size:24 final size:26
Alignment explanation
Indices: 519628--519686 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 26
519618 AAAATTTTAA
*
519628 AAAAATATTAAAGTAATATATATTCT
1 AAAAATATTAAAGTAAAATATATTCT
*
519654 --AAGTA-TAAA-TAAAATATATT-T
1 AAAAATATTAAAGTAAAATATATTCT
519675 AAAAATATTAAA
1 AAAAATATTAAA
519687 ATTATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
21 1 0.04
22 10 0.37
23 8 0.30
24 8 0.30
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (26 bp):
AAAAATATTAAAGTAAAATATATTCT
Found at i:520794 original size:22 final size:22
Alignment explanation
Indices: 520766--520810 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
520756 GGGTAAATCA
520766 TCGTCAAGTGGCTACATGGAAG
1 TCGTCAAGTGGCTACATGGAAG
520788 TCGTCAAGTGGCTACATGGAAG
1 TCGTCAAGTGGCTACATGGAAG
520810 T
1 T
520811 AGGTGACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (22 bp):
TCGTCAAGTGGCTACATGGAAG
Found at i:522390 original size:26 final size:27
Alignment explanation
Indices: 522355--522413 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
522345 ATCAAATTAC
522355 TATTTTATAAATAAA-TTAAA-AAATAA
1 TATTTTATAAATAAATTTAAATAAA-AA
*
522381 TATTTTATAATTAAATTTAAATAAAAA
1 TATTTTATAAATAAATTTAAATAAAAA
522408 TATTTT
1 TATTTT
522414 TATTATTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 14 0.47
27 13 0.43
28 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TATTTTATAAATAAATTTAAATAAAAA
Found at i:522400 original size:27 final size:26
Alignment explanation
Indices: 522355--522422 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
522345 ATCAAATTAC
*
522355 TATTTTATAAATAAATTAAA-AAATAA
1 TATTTTATAATTAAATTAAATAAA-AA
522381 TATTTTATAATTAAATTTAAATAAAAA
1 TATTTTATAATTAAA-TTAAATAAAAA
*
522408 TATTTTTATTATTAA
1 TA-TTTTATAATTAA
522423 CTAATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 14 0.38
27 9 0.24
28 14 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTTTATAATTAAATTAAATAAAAA
Found at i:526980 original size:52 final size:53
Alignment explanation
Indices: 526924--527024 Score: 120
Period size: 52 Copynumber: 1.9 Consensus size: 53
526914 ATACTTTAAT
*
526924 AAATTCTTT-CATAATGGAAAAATAAAATTTATA-ACATA-ATATAA-AAGTGATA
1 AAATT-TTTGCATAAT-GAAAAA-AAAATATATATACATATATATAATAAGTGATA
* *
526976 AAATTTTTGCATAATTAAAAAAAAATATATATATATATATATAATAAGT
1 AAATTTTTGCATAATGAAAAAAAAATATATATACATATATATAATAAGT
527025 TTAAGCAACG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
50 9 0.21
51 12 0.29
52 17 0.40
53 4 0.10
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (53 bp):
AAATTTTTGCATAATGAAAAAAAAATATATATACATATATATAATAAGTGATA
Found at i:527629 original size:22 final size:23
Alignment explanation
Indices: 527587--527641 Score: 85
Period size: 22 Copynumber: 2.3 Consensus size: 23
527577 TAAATTGTTA
527587 ATTATTAAAATATTAAAAATAATTT
1 ATTATTAAAATATT--AAATAATTT
527612 ATTATTAAAATATT-AATAATTT
1 ATTATTAAAATATTAAATAATTT
527634 ATTATTAA
1 ATTATTAA
527642 TATTTCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.53
25 14 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTATTAAAATATTAAATAATTT
Found at i:527917 original size:29 final size:27
Alignment explanation
Indices: 527894--527944 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
527884 TAATATTTTA
*
527894 ATAATAATATTTAATAC-TAAAATATT
1 ATAATAATATTAAATACTTAAAATATT
*
527920 ATATTAATATTAAATACTTAAAATA
1 ATAATAATATTAAATACTTAAAATA
527945 ATAATATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (27 bp):
ATAATAATATTAAATACTTAAAATATT
Found at i:528099 original size:16 final size:17
Alignment explanation
Indices: 528078--528110 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
528068 ATTAAATATG
528078 TATAAA-TTATAATTTT
1 TATAAATTTATAATTTT
528094 TATAAATTTATAATTTT
1 TATAAATTTATAATTTT
528111 ATTATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATAAATTTATAATTTT
Found at i:528202 original size:3 final size:3
Alignment explanation
Indices: 528194--528251 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
528184 ATGTTACGTT
528194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
528242 TTA TTA TTA T
1 TTA TTA TTA T
528252 CGTTGTTATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:529230 original size:22 final size:23
Alignment explanation
Indices: 529198--529241 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
529188 AATTTTTAAT
*
529198 TATTTGTAAAATATATAAATAAA
1 TATTTGTAAAATATAAAAATAAA
529221 TATTT-TAAAATATAAAAATAA
1 TATTTGTAAAATATAAAAATAA
529242 TAGATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TATTTGTAAAATATAAAAATAAA
Found at i:530318 original size:3 final size:3
Alignment explanation
Indices: 530312--530344 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
530302 TTCTTTAGTT
530312 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
530345 ACTTTCTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:533935 original size:141 final size:141
Alignment explanation
Indices: 533769--534036 Score: 509
Period size: 141 Copynumber: 1.9 Consensus size: 141
533759 TTTTTCACAC
533769 CTCAAAGTTTATTCTAGAACTCTTGCTCTCTAAAATTTCTTACATTGTGTACGCGAATTAAAATC
1 CTCAAAGTTTATTCTAGAACTCTTGCTCTCTAAAATTTCTTACATTGTGTACGCGAATTAAAATC
*
533834 ACTGCAAGGTTTGCTTAAAGGTGTAGTAATCAACAGACCTGATGATCAGGAAAGGGAACAAAGTA
66 ACTGCAAGGTTTGCTTAAAGGTGTAGTAATCAAAAGACCTGATGATCAGGAAAGGGAACAAAGTA
533899 TTTTTTTACGT
131 TTTTTTTACGT
* *
533910 CTCAAAGTTTATTTTAGAACTCTTGCTCTCTAAAATTTCTTACATTGTGTACGTGAATTAAAATC
1 CTCAAAGTTTATTCTAGAACTCTTGCTCTCTAAAATTTCTTACATTGTGTACGCGAATTAAAATC
533975 ACTGCAAGGTTTGCTTAAAGGTGTAGTAATCAAAAGACCTGATGATCAGGAAAGGGAACAAA
66 ACTGCAAGGTTTGCTTAAAGGTGTAGTAATCAAAAGACCTGATGATCAGGAAAGGGAACAAA
534037 TTTATCGTTT
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 124 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (141 bp):
CTCAAAGTTTATTCTAGAACTCTTGCTCTCTAAAATTTCTTACATTGTGTACGCGAATTAAAATC
ACTGCAAGGTTTGCTTAAAGGTGTAGTAATCAAAAGACCTGATGATCAGGAAAGGGAACAAAGTA
TTTTTTTACGT
Found at i:539647 original size:43 final size:43
Alignment explanation
Indices: 539600--539762 Score: 113
Period size: 43 Copynumber: 3.7 Consensus size: 43
539590 TATTGAATTC
*
539600 AATAATTATTATAATATATG-AAAAAAATTTTAAAAAAACTCAT
1 AATAAATATTATAATATATGTAAAAAAATTTTAAAAAAA-TCAT
* ***
539643 AATAAATATTAGT-ATTTATGTCAAAAATTAATATTATATATGGAAT--T
1 AATAAATATTA-TAATATATGT-AAAAA--AAT-TT-TA-AAAAAATCAT
*
539690 CAATAAATTATTATAATATATG-AAAAAAGTTTTGAAAAAAATCAT
1 -AATAAA-TATTATAATATATGTAAAAAAATTTT-AAAAAAATCAT
*
539735 AATAAATATTA-AGATTTATGTAAAAAAA
1 AATAAATATTATA-ATATATGTAAAAAAA
539763 ACTGTATATT
Statistics
Matches: 92, Mismatches: 12, Indels: 31
0.68 0.09 0.23
Matches are distributed among these distances:
42 1 0.01
43 32 0.35
44 16 0.17
45 8 0.09
47 9 0.10
48 9 0.10
49 14 0.15
50 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (43 bp):
AATAAATATTATAATATATGTAAAAAAATTTTAAAAAAATCAT
Found at i:539740 original size:92 final size:91
Alignment explanation
Indices: 539576--539761 Score: 304
Period size: 92 Copynumber: 2.0 Consensus size: 91
539566 TAAATTAGTG
*
539576 AAATTAATATTATATATTGAATTCAATAATTATTATAATATATGAAAAAAATTTTAAAAAAACTC
1 AAATTAATATTATATATGGAATTCAATAATTATTATAATATATGAAAAAAATTTTAAAAAAACTC
*
539641 ATAATAAATATT-AGTATTTATGTCAA
66 ATAATAAATATTAAG-ATTTATGTAAA
*
539667 AAATTAATATTATATATGGAATTCAATAAATTATTATAATATATGAAAAAAGTTTTGAAAAAAA-
1 AAATTAATATTATATATGGAATTCAAT-AATTATTATAATATATGAAAAAAATTTT-AAAAAAAC
539731 TCATAATAAATATTAAGATTTATGTAAA
64 TCATAATAAATATTAAGATTTATGTAAA
539759 AAA
1 AAA
539762 AACTGTATAT
Statistics
Matches: 89, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
91 26 0.29
92 54 0.61
93 9 0.10
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (91 bp):
AAATTAATATTATATATGGAATTCAATAATTATTATAATATATGAAAAAAATTTTAAAAAAACTC
ATAATAAATATTAAGATTTATGTAAA
Found at i:542265 original size:20 final size:20
Alignment explanation
Indices: 542242--542279 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
542232 TCTTTTTGTA
542242 TATATAAATACATAATAAAT
1 TATATAAATACATAATAAAT
*
542262 TATATGAATACATAATAA
1 TATATAAATACATAATAA
542280 TAATACAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (20 bp):
TATATAAATACATAATAAAT
Found at i:544397 original size:42 final size:42
Alignment explanation
Indices: 544336--544467 Score: 185
Period size: 42 Copynumber: 3.1 Consensus size: 42
544326 TAGCCCTCAA
* *
544336 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
* *
544378 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
* * *
544420 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAGGAGAGAAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGA-GAGACAAG
544463 A-AGAT
1 AGAGAT
544468 GGAAGAGTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 73 0.91
43 7 0.09
ACGTcount: A:0.45, C:0.02, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
Found at i:544415 original size:24 final size:24
Alignment explanation
Indices: 544345--544430 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
544335 AAGAGAAAGA
* *
544345 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGAGATGATAGGAGG
*
544369 AGAGACA--AGAGA-GAT---AGT
1 AGAGACAGGAGAGATGATAGGAGG
* *
544387 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGAGATGATAGGAGG
*
544411 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGAGATGATAG
544431 AGAGAGGAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 8 0.17
20 4 0.09
21 6 0.13
22 4 0.09
24 25 0.53
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGAGATGATAGGAGG
Found at i:550815 original size:52 final size:52
Alignment explanation
Indices: 550735--550854 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
550725 AAAAGTTGCT
*
550735 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
*
550787 TGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATT-TAATAATGTATCGATACATCTGGGCAAATTTACC
550839 TGCATGTATCGATACA
1 TGCATGTATCGATACA
550855 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 62 0.95
53 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
Found at i:550867 original size:52 final size:50
Alignment explanation
Indices: 550730--550874 Score: 184
Period size: 52 Copynumber: 2.8 Consensus size: 50
550720 ATATGAAAAG
* *
550730 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
* *
550782 TTACCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AATAGTGTATCGATACATCTGGGCAAAT
550834 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
550875 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
52 78 0.94
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:550881 original size:13 final size:13
Alignment explanation
Indices: 550863--550887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
550853 CAAAGATCAG
550863 TGTATCGATACAA
1 TGTATCGATACAA
550876 TGTATCGATACA
1 TGTATCGATACA
550888 TTTTTTTGGC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:550949 original size:13 final size:13
Alignment explanation
Indices: 550931--550955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
550921 AAAAAAAATA
550931 TGTATCGATACAT
1 TGTATCGATACAT
550944 TGTATCGATACA
1 TGTATCGATACA
550956 ACATTTTATG
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:553436 original size:21 final size:22
Alignment explanation
Indices: 553412--553454 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
553402 CTTGTTTACC
553412 TAATA-CATCACCTAACACACT
1 TAATAGCATCACCTAACACACT
*
553433 TAATATGCTTCACCTAACACAC
1 TAATA-GCATCACCTAACACAC
553455 CACCTAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.26
Consensus pattern (22 bp):
TAATAGCATCACCTAACACACT
Found at i:553448 original size:35 final size:34
Alignment explanation
Indices: 553409--553489 Score: 117
Period size: 35 Copynumber: 2.4 Consensus size: 34
553399 TATCTTGTTT
*
553409 ACCTAATACATCACCTAACACACTTAATATGCTTC
1 ACCTAATACACCACCTAACACACTTAATATGC-TC
* *
553444 ACCTAACACACCACCTAACACATTTAATATGCTC
1 ACCTAATACACCACCTAACACACTTAATATGCTC
*
553478 ACTTAATACACC
1 ACCTAATACACC
553490 TAATATGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 12 0.29
35 29 0.71
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.26
Consensus pattern (34 bp):
ACCTAATACACCACCTAACACACTTAATATGCTC
Found at i:553510 original size:22 final size:22
Alignment explanation
Indices: 553455--553510 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
553445 CCTAACACAC
**
553455 CACCTAACACATTTAATATGCT
1 CACCTAACACACCTAATATGCT
* * *
553477 CACTTAATACACCTAATATGTT
1 CACCTAACACACCTAATATGCT
*
553499 TACCTAACACAC
1 CACCTAACACAC
553511 TTAACAAAGA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.30
Consensus pattern (22 bp):
CACCTAACACACCTAATATGCT
Found at i:556775 original size:34 final size:34
Alignment explanation
Indices: 556737--556803 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
556727 AAATATCTTG
* *
556737 CTCACCTAACACATTATCTAACACACCTAATATA
1 CTCACCTAACACATCACCTAACACACCTAATATA
*
556771 CTCACCTAACACATCACCTAACGCACCTAATAT
1 CTCACCTAACACATCACCTAACACACCTAATAT
556804 GCTTCACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.36, G:0.01, T:0.24
Consensus pattern (34 bp):
CTCACCTAACACATCACCTAACACACCTAATATA
Found at i:556837 original size:22 final size:22
Alignment explanation
Indices: 556784--556863 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
556774 ACCTAACACA
*
556784 TCACCTAACGCACCTAATATGC
1 TCACCTAACACACCTAATATGC
* *
556806 TTCACTTAACATACCTAATATGC
1 -TCACCTAACACACCTAATATGC
*
556829 TCACCTAACACACCTAATATGT
1 TCACCTAACACACCTAATATGC
*
556851 TTACCTAACACAC
1 TCACCTAACACAC
556864 TTAACAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 31 0.62
23 19 0.38
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (22 bp):
TCACCTAACACACCTAATATGC
Found at i:558543 original size:22 final size:22
Alignment explanation
Indices: 558504--558545 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
558494 TATTTTTACT
558504 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
*
558526 TAAATATTAA-TATTAAAATA
1 TAAAT-TTAATTATAAAAATA
558546 AATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:558892 original size:19 final size:19
Alignment explanation
Indices: 558870--558906 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
558860 ATAGATAAAA
558870 ATTAAATTTATATATTTTT
1 ATTAAATTTATATATTTTT
*
558889 ATTATATTTATATATTTT
1 ATTAAATTTATATATTTT
558907 ATGATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTAAATTTATATATTTTT
Found at i:559355 original size:13 final size:13
Alignment explanation
Indices: 559339--559364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
559329 AAAAAATAAA
559339 AAATTAAAAAAAT
1 AAATTAAAAAAAT
559352 AAATTAAAAAAAT
1 AAATTAAAAAAAT
559365 TTATATATTT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATTAAAAAAAT
Found at i:559417 original size:21 final size:22
Alignment explanation
Indices: 559387--559437 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
559377 CGTATATTTT
*
559387 ATAATATTATAATCATATTTAA
1 ATAATTTTATAATCATATTTAA
* * *
559409 AT-ATTTTATATTTATATTTAT
1 ATAATTTTATAATCATATTTAA
559430 ATAATTTT
1 ATAATTTT
559438 TTATAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAATTTTATAATCATATTTAA
Found at i:559654 original size:17 final size:17
Alignment explanation
Indices: 559628--559662 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
559618 ATTTATATGA
*
559628 TATTCGAATATATTTAT
1 TATTCAAATATATTTAT
559645 TATTCAAATATATTTAT
1 TATTCAAATATATTTAT
559662 T
1 T
559663 TGAATCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (17 bp):
TATTCAAATATATTTAT
Found at i:559958 original size:31 final size:32
Alignment explanation
Indices: 559915--559980 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
559905 ATCGATTACG
559915 AATATTAATAAATTTAT-TATTTAAATTTAAA
1 AATATTAATAAATTTATATATTTAAATTTAAA
*
559946 AATATTATTAAATTTATAATATTTAAATTTAAA
1 AATATTAATAAATTTAT-ATATTTAAATTTAAA
559979 AA
1 AA
559981 AAAACAGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 16 0.50
33 16 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
AATATTAATAAATTTATATATTTAAATTTAAA
Found at i:561274 original size:3 final size:3
Alignment explanation
Indices: 561266--561307 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
561256 AAGAAAACAT
561266 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
561308 GAAAAAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:561561 original size:2 final size:2
Alignment explanation
Indices: 561549--561588 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
561539 ATTCATTCAT
* * *
561549 TA TA TA CA TA TA TA TA TA TA TA TG TA TA TA AA 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
561589 AACACACTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:564117 original size:22 final size:22
Alignment explanation
Indices: 564089--564130 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
564079 TTTATATAAG
564089 ATATGTTCACCTAACACACCTA
1 ATATGTTCACCTAACACACCTA
* *
564111 ATATGTTTACTTAACACACC
1 ATATGTTCACCTAACACACC
564131 ACCTAACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.31
Consensus pattern (22 bp):
ATATGTTCACCTAACACACCTA
Found at i:564139 original size:34 final size:34
Alignment explanation
Indices: 564096--564200 Score: 120
Period size: 34 Copynumber: 3.0 Consensus size: 34
564086 AAGATATGTT
*
564096 CACCTAACACACCTAATATGTTTACTTAACACAC
1 CACCTAACACACCTAATATGTTTACCTAACACAC
* * *
564130 CACCTAACACACTTAATATATTATTCACCTAACATAC
1 CACCTAACACACCTAATAT-GT-TT-ACCTAACACAC
* **
564167 TACCTAACTTACCTAATATGTTTACCTAACACAC
1 CACCTAACACACCTAATATGTTTACCTAACACAC
564201 TTAATAAAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
34 28 0.48
35 3 0.05
36 3 0.05
37 24 0.41
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (34 bp):
CACCTAACACACCTAATATGTTTACCTAACACAC
Found at i:571219 original size:13 final size:13
Alignment explanation
Indices: 571201--571225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
571191 TACAAAGATC
571201 AATGTATCGATAA
1 AATGTATCGATAA
571214 AATGTATCGATA
1 AATGTATCGATA
571226 CATTGAGTAA
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAA
Found at i:571224 original size:33 final size:33
Alignment explanation
Indices: 571182--571245 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
571172 AAATTCCCAG
571182 ATGTATCGATACAAAGA-TCAATGTATCGATAAA
1 ATGTATCGATACAAAGAGT-AATGTATCGATAAA
**
571215 ATGTATCGATACATTGAGTAATGTATCGATA
1 ATGTATCGATACAAAGAGTAATGTATCGATA
571246 CATTTCCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATAAA
Found at i:571289 original size:13 final size:13
Alignment explanation
Indices: 571271--571322 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
571261 AGCTTCGTAG
571271 CGATACATTGTAT
1 CGATACATTGTAT
571284 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
571303 CGATACATTGTAT
1 CGATACATTGTAT
571316 CGATACA
1 CGATACA
571323 ACACTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:571303 original size:19 final size:19
Alignment explanation
Indices: 571279--571341 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
571269 AGCGATACAT
571279 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
571298 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
571311 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
571330 TATATCGATACA
1 TGTATCGATACA
571342 GTTATTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 20 0.54
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:571312 original size:32 final size:32
Alignment explanation
Indices: 571271--571341 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
571261 AGCTTCGTAG
*
571271 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATATAT
571303 CGATACATTGTATCGATACAACACTTATATAT
1 CGATACATTGTATCGATACAACACTTATATAT
571335 CGATACA
1 CGATACA
571342 GTTATTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATATAT
Found at i:573852 original size:19 final size:19
Alignment explanation
Indices: 573828--573864 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
573818 TCAAATCTTT
*
573828 TTTGTTTCTAGATTTAATA
1 TTTGTTTATAGATTTAATA
*
573847 TTTGTTTATATATTTAAT
1 TTTGTTTATAGATTTAAT
573865 TATTATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTGTTTATAGATTTAATA
Found at i:573871 original size:11 final size:12
Alignment explanation
Indices: 573852--573883 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
573842 TAATATTTGT
573852 TTATATATTTAA
1 TTATATATTTAA
573864 TTAT-TATTTAA
1 TTATATATTTAA
573875 TT-TATATTT
1 TTATATATTT
573884 TATTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 14 0.74
12 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATATTTAA
Found at i:573885 original size:12 final size:13
Alignment explanation
Indices: 573839--573889 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 13
573829 TTGTTTCTAG
573839 ATTTA-ATATTT-
1 ATTTATATATTTA
*
573850 GTTTATATATTTA
1 ATTTATATATTTA
573863 A-TTAT-TATTTA
1 ATTTATATATTTA
573874 ATTTATAT-TTT-
1 ATTTATATATTTA
573885 ATTTA
1 ATTTA
573890 AAAAACTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 16 0.47
12 17 0.50
13 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
ATTTATATATTTA
Found at i:573886 original size:16 final size:16
Alignment explanation
Indices: 573858--573890 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
573848 TTGTTTATAT
573858 ATTTAATTATTATTTA
1 ATTTAATTATTATTTA
573874 ATTTATATT-TTATTTA
1 ATTTA-ATTATTATTTA
573890 A
1 A
573891 AAAACTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTAATTATTATTTA
Found at i:575513 original size:20 final size:21
Alignment explanation
Indices: 575488--575544 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
575478 AAAACCCTTA
575488 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACATAATTGC
*
575508 AAAGTATCGATACAT-GTTGC
1 AAAGTATCGATACATAATTGC
* *
575528 AATGTATCGTTACATAA
1 AAAGTATCGATACATAA
575545 AAAATATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (21 bp):
AAAGTATCGATACATAATTGC
Found at i:575632 original size:13 final size:13
Alignment explanation
Indices: 575614--575639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
575604 ACACCAAAGT
575614 ATGTATCGATACA
1 ATGTATCGATACA
575627 ATGTATCGATACA
1 ATGTATCGATACA
575640 CAAAAAATTG
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:581617 original size:8 final size:8
Alignment explanation
Indices: 581604--581635 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
581594 ATTTGATTAA
581604 ATTTTGTG
1 ATTTTGTG
581612 ATTTTGTG
1 ATTTTGTG
581620 ATTTTGTG
1 ATTTTGTG
581628 ATTTTGTG
1 ATTTTGTG
581636 TTGAATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:582026 original size:20 final size:20
Alignment explanation
Indices: 581983--582028 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
581973 AAATCTTTTG
581983 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
582004 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
582024 CAAAA
1 CAAAA
582029 CCAACATCAA
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:584337 original size:20 final size:20
Alignment explanation
Indices: 584312--584366 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
584302 AAAACCCTTA
584312 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
*
584332 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
584352 AATGTATCGATACAT
1 AAAGTATCGATACAT
584367 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:584444 original size:20 final size:20
Alignment explanation
Indices: 584418--584470 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
584408 GTAGCCAAAC
* *
584418 TTGTATCGATACAC-CAAAG
1 TTGTATCGATACACAAAAAA
584437 TATGTATCGATACACAAAAAA
1 T-TGTATCGATACACAAAAAA
584458 TTGTATCGATACA
1 TTGTATCGATACA
584471 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:587668 original size:13 final size:13
Alignment explanation
Indices: 587650--587675 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
587640 TACACACAAG
587650 ATGTATCGATACA
1 ATGTATCGATACA
587663 ATGTATCGATACA
1 ATGTATCGATACA
587676 TCCCAAAATG
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:587692 original size:33 final size:32
Alignment explanation
Indices: 587632--587695 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
587622 CTTAACTGTT
*
587632 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
587664 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
587696 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:593854 original size:13 final size:13
Alignment explanation
Indices: 593836--593873 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
593826 CAACATTCTC
*
593836 TGTATCGATACAT
1 TGTATCGATACAG
593849 TGTATCGATACAG
1 TGTATCGATACAG
593862 TGTATCGATACA
1 TGTATCGATACA
593874 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:595217 original size:20 final size:20
Alignment explanation
Indices: 595192--595246 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
595182 AAAACCCTTA
595192 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
*
595212 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
595232 AATGTATCGATACAT
1 AAAGTATCGATACAT
595247 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:602807 original size:52 final size:52
Alignment explanation
Indices: 602737--602857 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
602727 GAAAATTTAT
*
602737 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
602789 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
602841 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
602858 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:602870 original size:52 final size:51
Alignment explanation
Indices: 602737--602877 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
602727 GAAAATTTAT
602737 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
602789 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
602841 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
602878 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:602884 original size:13 final size:13
Alignment explanation
Indices: 602866--602890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
602856 CAAAGATCAG
602866 TGTATCGATACAA
1 TGTATCGATACAA
602879 TGTATCGATACA
1 TGTATCGATACA
602891 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:602978 original size:33 final size:33
Alignment explanation
Indices: 602933--602999 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
602923 AGTAGCTTAA
602933 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* * ***
602966 ATTGTATTGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
602999 A
1 A
603000 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:604091 original size:174 final size:174
Alignment explanation
Indices: 603801--604193 Score: 732
Period size: 174 Copynumber: 2.3 Consensus size: 174
603791 AGAGATGATG
*
603801 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGATGATGAGAAAAGTGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGA
603866 TAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTC
66 TAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTC
*
603931 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
131 AACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
*
603975 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGA
*
604040 TAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTC
66 TAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTC
604105 AACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
131 AACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
* *
604149 AATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAA
604194 GGTGCCAATG
Statistics
Matches: 213, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 213 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (174 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGA
TAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGATGTC
AACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
Found at i:604251 original size:49 final size:49
Alignment explanation
Indices: 604109--604571 Score: 557
Period size: 49 Copynumber: 9.7 Consensus size: 49
604099 GATGTCAACG
* *
604109 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
604161 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
604204 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
604253 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
604296 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
604345 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
604388 TGCTGAATCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * * *
604437 TGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
604486 TGCTGAGTCAAGGCCAACTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* *
604538 TGCTGATTCAAGGCCAGCTATATTGGGCTTAAAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
604572 GGGTTGCCAC
Statistics
Matches: 355, Mismatches: 35, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
43 105 0.30
44 8 0.02
45 3 0.01
46 5 0.01
47 2 0.01
48 8 0.02
49 151 0.43
50 2 0.01
51 2 0.01
52 69 0.19
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:604282 original size:92 final size:92
Alignment explanation
Indices: 604108--604572 Score: 732
Period size: 92 Copynumber: 4.9 Consensus size: 92
604098 GGATGTCAAC
* *
604108 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATATGCTGATTCAAG
*
604173 GCCAGCTATATTGGACTTAAAGGTGCCAAT
63 GCCAGCGATATTGGACTTAAAGGTGCCAAT
604203 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
604268 AGCGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
604295 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
604360 AGCGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
* *
604387 GTGCTGAATCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGTTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
604452 AGCGATATTGGACTTAAAGATGAAGGTGCCAAT
66 AGCGATATTGGACTT----A--AAGGTGCCAAT
* * *
604485 GTGCTGAGTCAAGGCCAACTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAG
* *
604550 GCCAGCTATATTGGGCTTAAAGG
63 GCCAGCGATATTGGACTTAAAGG
604573 GGTTGCCACC
Statistics
Matches: 350, Mismatches: 11, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
92 219 0.63
94 4 0.01
95 40 0.11
96 1 0.00
97 1 0.00
98 46 0.13
99 1 0.00
101 38 0.11
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGGTGCCAAT
Found at i:604702 original size:71 final size:71
Alignment explanation
Indices: 604642--605746 Score: 1344
Period size: 71 Copynumber: 16.0 Consensus size: 71
604632 GGGAAGGGAG
* * *
604642 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGAGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
604705 AA-GAA
66 AAGGAA
*
604710 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
604775 ACA-GAA
66 A-AGGAA
*
604781 AAAGGTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
604846 ACGGAA
66 AAGGAA
* **
604852 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
604917 AA-GAA
66 AAGGAA
* * * *
604922 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACCGACTTGTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTT
* *
604984 TAGGAAGGGAG
63 TA--AAAGGAA
* *
604995 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
605058 AA-GAA
66 AAGGAA
*
605063 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
605128 ACA-GAA
66 A-AGGAA
605134 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
605199 ACGGAA
66 AAGGAA
* ** *
605205 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTATGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
605270 AA-GAA
66 AAGGAA
* * * *
605275 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACCGACTTGTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTT
* *
605337 TAGGAAGGGAG
63 TA--AAAGGAA
* *
605348 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
605411 AA-GAA
66 AAGGAA
*
605416 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
605481 ACA-GAA
66 A-AGGAA
* **
605487 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
605552 AA-GAA
66 AAGGAA
* * *
605557 GAAGGTGCCATGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGC-TT-A
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
605617 AACG--
66 AAGGAA
* * * *
605621 ---GGTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAA-AGTGCCACAGAATTGTGGGCTTTA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
605679 AAA-G--
65 AAAGGAA
* * * *
605683 ---GGTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAAAAGTGCCACGGAATTGTGGGCTTTA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
605742 AAAGG
65 AAAGG
605747 GTGCCACGGA
Statistics
Matches: 925, Mismatches: 74, Indels: 80
0.86 0.07 0.07
Matches are distributed among these distances:
58 3 0.00
60 2 0.00
61 40 0.04
62 37 0.04
63 29 0.03
64 1 0.00
65 3 0.00
66 3 0.00
67 19 0.02
68 93 0.10
69 12 0.01
70 236 0.26
71 363 0.39
72 10 0.01
73 72 0.08
74 2 0.00
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (71 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AAGGAA
Found at i:604828 original size:141 final size:141
Alignment explanation
Indices: 604642--605743 Score: 1394
Period size: 141 Copynumber: 8.0 Consensus size: 141
604632 GGGAAGGGAG
* * *
604642 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGAGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
604705 AAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
66 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
604770 TTTAAACAGAA
131 TTTAAACAGAA
*
604781 AAAGGTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * **
604846 ACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGG
66 A-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
604911 CTTTAAA-AGAA
130 CTTTAAACAGAA
* * * *
604922 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACCGACTTGTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTT
* * * *
604984 TAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTT
63 TA--AA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTT
605047 GTGGGCTTTAAA-AGAA
125 GTGGGCTTTAAACAGAA
*
605063 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
605128 ACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
66 A-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
*
605193 CTTTAAACGGAA
130 CTTTAAACAGAA
* ** *
605205 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTATGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * * *
605270 AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACCGACTTGTGTG
66 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG-TGCCACGGA-GT-TGTG
** *
605332 GGCTTTAGGAAGGGAG
128 GGCTTTA--AACAGAA
* *
605348 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
605411 AAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
66 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
605476 TTTAAACAGAA
131 TTTAAACAGAA
* **
605487 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * *
605552 AAGAAGAAGGTGCCATGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGC
66 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
605614 -TTAAAC-G--
131 TTTAAACAGAA
* * * *
605621 ---GGTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAA-AGTGCCACAGAATTGTGGGCTTTA
1 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
* * * *
605679 AAAG-----GGTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAAAAGTGCCACGGAATTGTGG
65 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGG
605736 GCTTTAAA
129 GCTTTAAA
605744 AGGGTGCCAC
Statistics
Matches: 857, Mismatches: 76, Indels: 74
0.85 0.08 0.07
Matches are distributed among these distances:
120 3 0.00
122 2 0.00
123 23 0.03
124 18 0.02
125 5 0.01
128 30 0.04
129 5 0.01
130 2 0.00
131 19 0.02
136 1 0.00
137 6 0.01
138 21 0.02
139 104 0.12
140 8 0.01
141 393 0.46
142 135 0.16
143 80 0.09
144 2 0.00
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (141 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
TTTAAACAGAA
Found at i:605246 original size:353 final size:353
Alignment explanation
Indices: 604600--605745 Score: 1890
Period size: 353 Copynumber: 3.3 Consensus size: 353
604590 GTGGGCTTTG
*
604600 GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTGGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC
1 GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC
*
604665 TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGAGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTG
66 TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTG
604730 GGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGA
131 GGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGA
*
604795 ATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGC
196 GTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGC
604860 CACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAA
261 CACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAA
604925 GGTGCCACGGAGTTGTGGGCTTTGAAAA
326 GGTGCCACGGAGTTGTGGGCTTTGAAAA
604953 GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC
1 GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC
605018 TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTG
66 TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTG
605083 GGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGA
131 GGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGA
605148 GTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGC
196 GTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGC
*
605213 CACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTATGGGCTTTAAAAGAAGAA
261 CACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAA
605278 GGTGCCACGGAGTTGTGGGCTTTGAAAA
326 GGTGCCACGGAGTTGTGGGCTTTGAAAA
605306 GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC
1 GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC
605371 TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTG
66 TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTG
605436 GGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGA
131 GGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGA
* ** * *
605501 GTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAA-AGAAGAAGGTGC
196 GTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGC
* * ** *
605565 CATGGAGTTGTGGGCTTTGAAAA-G-AAGAAG-GTGCCACGGAGTTGTGGGC-TT--AA-ACG--
261 CACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAA
*
605621 GGTGCCACGGAGTTGTGGAC-TT-AAAGA
326 GGTGCCACGGAGTTGTGGGCTTTGAAA-A
* * * * *
605648 TGAAAAAAG-TGCCACAGA-AT-TGTGGGCTTTA--AA---AG---GGTGCCACGGAGTTGTGGA
1 -GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGA
* * *
605702 CTT-AAAGATGAAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAG
65 CTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
605746 GGTGCCACGG
Statistics
Matches: 766, Mismatches: 24, Indels: 27
0.94 0.03 0.03
Matches are distributed among these distances:
331 4 0.01
332 54 0.07
335 2 0.00
338 2 0.00
340 11 0.01
341 4 0.01
342 11 0.01
343 25 0.03
345 2 0.00
346 2 0.00
348 2 0.00
349 16 0.02
350 5 0.01
351 1 0.00
352 32 0.04
353 593 0.77
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (353 bp):
GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC
TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTG
GGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGA
GTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGC
CACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAA
GGTGCCACGGAGTTGTGGGCTTTGAAAA
Found at i:605632 original size:27 final size:26
Alignment explanation
Indices: 605594--605708 Score: 95
Period size: 27 Copynumber: 4.0 Consensus size: 26
605584 AAAAGAAGAA
*
605594 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAA-G
605621 GGTGCCACGGAGTTGTGGACTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAG
* * *
605647 ATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAG
1 --G------GTGCCACGGAGTTGTGGAC-TT-AAAG
605683 GGTGCCACGGAGTTGTGGACTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAG
605709 ATGAAAAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
26 5 0.07
27 26 0.37
28 17 0.24
34 17 0.24
35 2 0.03
36 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.23
Consensus pattern (26 bp):
GGTGCCACGGAGTTGTGGACTTAAAG
Found at i:605690 original size:28 final size:28
Alignment explanation
Indices: 605594--605771 Score: 133
Period size: 28 Copynumber: 5.9 Consensus size: 28
605584 AAAAGAAGAA
* *
605594 GGTGCCACGGAGTTGTGGGC-TTAAACG
1 GGTGCCACGGAATTGTGGGCTTTAAAAG
* * *
605621 GGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA
1 GGTGCCACGGAATTGTGGGCTT-----T-AAAAG
* *
605655 AGTGCCACAGAATTGTGGGCTTTAAAAG
1 GGTGCCACGGAATTGTGGGCTTTAAAAG
* * *
605683 GGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
1 GGTGCCACGGAATTGTGGGCTT-----T--AAAAG
*
605718 AGTGCCACGGAATTGTGGGCTTTAAAAG
1 GGTGCCACGGAATTGTGGGCTTTAAAAG
605746 GGTGCCACGGAATTGTGGGCTTTAAA
1 GGTGCCACGGAATTGTGGGCTTTAAA
605772 GAAAAAATGC
Statistics
Matches: 119, Mismatches: 18, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
27 19 0.16
28 52 0.44
29 1 0.01
30 1 0.01
33 2 0.02
34 21 0.18
35 23 0.19
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (28 bp):
GGTGCCACGGAATTGTGGGCTTTAAAAG
Found at i:605749 original size:63 final size:63
Alignment explanation
Indices: 605485--605773 Score: 322
Period size: 63 Copynumber: 4.5 Consensus size: 63
605475 CTTTAAACAG
* * *
605485 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA-AGGAAAAAAGAGTGCCAC-AAAGTTGTGGGCT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTT-AAAGATG-AAAAA-AGTGCCACGGAA-TTGTGGGCT
605548 TT
62 TT
* * * *
605550 AAAAGAAGAAGGTGCCATGGAGTTGTGGGCTTTGAAA-A-GAAGAAGGTGCCACGGAGTTGTGGG
1 --AA-AAG--GGTGCCACGGAGTTGTGGGCTTT-AAAGATGAAAAAAGTGCCACGGAATTGTGGG
605613 C-TT
60 CTTT
* * *
605616 AAACGGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
*
605678 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAAGTGCCACGGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGATG-AAAAAAGTGCCACGGAATTGTGGGCTTT
*
605741 AAAAGGGTGCCACGGAATTGTGGGCTTTAAAGA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGA
605774 AAAAATGCCA
Statistics
Matches: 196, Mismatches: 17, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
59 3 0.02
60 3 0.02
61 40 0.20
62 35 0.18
63 52 0.27
64 9 0.05
66 2 0.01
67 17 0.09
68 7 0.04
69 1 0.01
70 27 0.14
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.22
Consensus pattern (63 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
Found at i:614148 original size:52 final size:52
Alignment explanation
Indices: 614078--614218 Score: 228
Period size: 52 Copynumber: 2.7 Consensus size: 52
614068 GAAAATTTAT
614078 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
614130 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
*** *
614182 CTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACA
614219 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:614225 original size:13 final size:13
Alignment explanation
Indices: 614207--614231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
614197 CAAAGATTAG
614207 TGTATCGATACAA
1 TGTATCGATACAA
614220 TGTATCGATACA
1 TGTATCGATACA
614232 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:614302 original size:20 final size:19
Alignment explanation
Indices: 614273--614310 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
614263 GCAGTAGCTT
614273 AAATTGTATCGATACAAAA
1 AAATTGTATCGATACAAAA
614292 AAATATGTATCGATACAAA
1 AAAT-TGTATCGATACAAA
614311 TCGTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
AAATTGTATCGATACAAAA
Found at i:616105 original size:13 final size:13
Alignment explanation
Indices: 616087--616123 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
616077 ACATTTTTCT
616087 TTGTATCGATACA
1 TTGTATCGATACA
616100 TTGTATCGATACA
1 TTGTATCGATACA
*
616113 CTGTATCGATA
1 TTGTATCGATA
616124 TAGGGGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:616289 original size:20 final size:20
Alignment explanation
Indices: 616246--616291 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
616236 AAATCTTTTG
616246 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
616267 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
616287 CAAAA
1 CAAAA
616292 CCAACATCAA
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:618609 original size:20 final size:20
Alignment explanation
Indices: 618584--618638 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
618574 AAAACCCTTA
618584 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
* *
618604 AAAGTATCGATATATGTTGC
1 AAAGTATCGATACATATTGC
*
618624 AATGTATCGATACAT
1 AAAGTATCGATACAT
618639 CAAAAATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:620330 original size:22 final size:21
Alignment explanation
Indices: 620305--620348 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
620295 AATTGTTATT
*
620305 AAATTGCTTTATTAAGTGGGAG
1 AAATT-CTTTATTAAGGGGGAG
*
620327 AAATTTTTTATTAAGGGGGAG
1 AAATTCTTTATTAAGGGGGAG
620348 A
1 A
620349 GATAAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (21 bp):
AAATTCTTTATTAAGGGGGAG
Found at i:620929 original size:13 final size:13
Alignment explanation
Indices: 620911--620935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
620901 ATAATGCACA
620911 GTATCGATACATT
1 GTATCGATACATT
620924 GTATCGATACAT
1 GTATCGATACAT
620936 GACCAAATGT
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):
GTATCGATACATT
Found at i:621053 original size:13 final size:13
Alignment explanation
Indices: 621035--621059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
621025 TACACACAAG
621035 ATGTATCGATACC
1 ATGTATCGATACC
621048 ATGTATCGATAC
1 ATGTATCGATAC
621060 ATCCCAAAAT
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACC
Found at i:621077 original size:33 final size:32
Alignment explanation
Indices: 621017--621079 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
621007 CTTAACTGTT
*
621017 TGTATCGATACACACAAGATGTATCGATACCA
1 TGTATCGATACACACAAAATGTATCGATACCA
*
621049 TGTATCGATACATCCCAAAATGTATCGATAC
1 TGTATCGATACA-CACAAAATGTATCGATAC
621080 ATTGGTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACCA
Found at i:622249 original size:146 final size:148
Alignment explanation
Indices: 621993--622621 Score: 384
Period size: 153 Copynumber: 4.1 Consensus size: 148
621983 AGGAGTACTT
*
621993 GATACCCTCAAAAGACTTAAAAAAATCATGAATGGGATGAACCTATCCTAAATATCTACCTTCGG
1 GATACCCTCAAAAGACTTAAAAAAATCATAAATGGGATGAACCTATCC-----ATCTACCTTCGG
* * ** *
622058 CATTAAAGCAGACCCGGTGATAACCTAGGACTTGGTTTTAGAAAATT-ATGAATGCCCCTAGGGG
61 CATAAAAGCAGACCCGGTGATAACCTAGGACTTGATTTTAGAAAATTAAAAAATGCCCATAGGGG
622122 ATACCTTCGACATAAAAGTACCC
126 ATACCTTCGACATAAAAGTACCC
*
622145 GATACCC-CTAAAAGACTTAAAAAGGATCATAAATGGGATGAACCTATCC-T-TACCTTCGGCAT
1 GATACCCTC-AAAAGACTTAAAAA-AATCATAAATGGGATGAACCTATCCATCTACCTTCGGCAT
* * *
622207 AAAAGCGGACCCGGTGATGACCTAGGAGTTGATTTT-GAAAAATTACAAAAATGCCCATAGGGGA
64 AAAAGCAGACCCGGTGATAACCTAGGACTTGATTTTAG-AAAATTA-AAAAATGCCCATAGGGGA
* ** **
622271 TATCTTCGATGTAAAAGTACTT
127 TACCTTCGACATAAAAGTACCC
* * * *** * * * *
622293 GATA-TCTCTAAAGGATTTGAAAAGGGTTAGGACAT--GAT-AACCTATCCTAGATATTTA-CTT
1 GATACCCTC-AAAAGACTT-AAAAAAATCA-TAAATGGGATGAACCTATCC-----ATCTACCTT
* * * * * * *
622353 TGGCATACAAGCAGACTCTGTGATAACCTAGGATTTGATTCTGAAAAAATTACAAAAATGCTCC-
58 CGGCATAAAAGCAGACCCGGTGATAACCTAGGACTTGATT-TTAGAAAATTA-AAAAATGC-CCA
** * * **
622417 TAGGGGATATTTTTGACGTAAAAGTACTT
120 TAGGGGATACCTTCGACATAAAAGTACCC
* * * * *
622446 GATACCC-CTAAAGGACGTAAAAAAGATAATAAATGAGATGAACCTATCCTAAATATCTACTTTC
1 GATACCCTC-AAAAGACTTAAAAAA-ATCATAAATGGGATGAACCTATCC-----ATCTACCTTC
* * * * * * * * *
622510 GGCATAAAAGCAGACTCGGTGACAACCTAAGACTCGGTTCTAAAAAATTACAAAAATACACATAG
59 GGCATAAAAGCAGACCCGGTGATAACCTAGGACTTGATTTTAGAAAATTA-AAAAATGCCCATAG
* * **
622575 GGGATACCCTT-AACGTAAAAGTATTC
123 GGGATA-CCTTCGACATAAAAGTACCC
* *
622601 GATACCCTTAAATGACTTAAA
1 GATACCCTCAAAAGACTTAAA
622622 GGATTTATAG
Statistics
Matches: 383, Mismatches: 67, Indels: 51
0.76 0.13 0.10
Matches are distributed among these distances:
145 1 0.00
146 58 0.15
147 5 0.01
148 48 0.13
149 7 0.02
151 1 0.00
152 65 0.17
153 83 0.22
154 7 0.02
155 72 0.19
156 36 0.09
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (148 bp):
GATACCCTCAAAAGACTTAAAAAAATCATAAATGGGATGAACCTATCCATCTACCTTCGGCATAA
AAGCAGACCCGGTGATAACCTAGGACTTGATTTTAGAAAATTAAAAAATGCCCATAGGGGATACC
TTCGACATAAAAGTACCC
Found at i:622438 original size:153 final size:154
Alignment explanation
Indices: 621943--622621 Score: 527
Period size: 152 Copynumber: 4.5 Consensus size: 154
621933 CTAAGTTTCA
* * * * ** *
621943 AAAAAATTACGAAAATACTCTTAGGGGATA-CTTTTGACGTAGGAGTACTTGATA-CCCTCAAAA
1 AAAAAATTACAAAAATGC-CCTAGGGGATATC-TTCGACGTAAAAGTACTTGATACCCCT-AAAG
* * * * *
622006 GACTTAAAAAA-ATCATG-AATGGGATGAACCTATCCTAAATATCTACCTTCGGCATTAAAGCAG
63 GACGTAAAAAAGAT-AAGAAAT-AGATGAACCTATCCTAAATATCTACTTTCGGCATAAAAGCAG
* * *
622069 ACCCGGTGATAACCTAGGACTTGGTT-TT
126 ACTCGGTGATAACCTAGGACTTGATTCTG
* ** * * ** *
622097 AGAAAATT--ATGAATGCCCCTAGGGGATACCTTCGACATAAAAGTACCCGATACCCCTAAAAGA
1 AAAAAATTACAAAAATG-CCCTAGGGGATATCTTCGACGTAAAAGTACTTGATACCCCTAAAGGA
* * * * * * *
622160 CTTAAAAAGGATCATAAATGGGATGAACCTATCCT---TA-C--C-TTCGGCATAAAAGCGGACC
65 CGTAAAAAAGATAAGAAAT-AGATGAACCTATCCTAAATATCTACTTTCGGCATAAAAGCAGACT
* * *
622218 CGGTGATGACCTAGGAGTTGATTTTG
129 CGGTGATAACCTAGGACTTGATTCTG
* * *
622244 -AAAAATTACAAAAATGCCCATAGGGGATATCTTCGATGTAAAAGTACTTGATATCTCTAAAGGA
1 AAAAAATTACAAAAATGCCC-TAGGGGATATCTTCGACGTAAAAGTACTTGATACCCCTAAAGGA
** ** * * * * * *
622308 TTTGAAAAGGGTTAGGACAT-GAT-AACCTATCCTAGATATTTACTTT-GGCATACAAGCAGACT
65 CGT-AAAAAAGATAAGAAATAGATGAACCTATCCTAAATATCTACTTTCGGCATAAAAGCAGACT
* *
622370 CTGTGATAACCTAGGATTTGATTCTG
129 CGGTGATAACCTAGGACTTGATTCTG
* *
622396 AAAAAATTACAAAAATGCTCCTAGGGGATATTTTTGACGTAAAAGTACTTGATACCCCTAAAGGA
1 AAAAAATTACAAAAATGC-CCTAGGGGATATCTTCGACGTAAAAGTACTTGATACCCCTAAAGGA
*
622461 CGTAAAAAAGATAATAAATGAGATGAACCTATCCTAAATATCTACTTTCGGCATAAAAGCAGACT
65 CGTAAAAAAGATAAGAAAT-AGATGAACCTATCCTAAATATCTACTTTCGGCATAAAAGCAGACT
* * * *
622526 CGGTGACAACCTAAGACTCGGTTCT-
129 CGGTGATAACCTAGGACTTGATTCTG
* * * * * *
622551 AAAAAATTACAAAAATACACATAGGGGATACCCTT-AACGTAAAAGTA-TTCGATACCCTTAAAT
1 AAAAAATTACAAAAATGC-CCTAGGGGATA-TCTTCGACGTAAAAGTACTT-GATACCCCTAAAG
*
622614 GACTTAAA
63 GACGTAAA
622622 GGATTTATAG
Statistics
Matches: 421, Mismatches: 79, Indels: 49
0.77 0.14 0.09
Matches are distributed among these distances:
146 53 0.13
147 8 0.02
148 43 0.10
149 13 0.03
150 2 0.00
152 89 0.21
153 86 0.20
154 14 0.03
155 77 0.18
156 36 0.09
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (154 bp):
AAAAAATTACAAAAATGCCCTAGGGGATATCTTCGACGTAAAAGTACTTGATACCCCTAAAGGAC
GTAAAAAAGATAAGAAATAGATGAACCTATCCTAAATATCTACTTTCGGCATAAAAGCAGACTCG
GTGATAACCTAGGACTTGATTCTG
Found at i:623247 original size:168 final size:167
Alignment explanation
Indices: 622725--623490 Score: 1153
Period size: 167 Copynumber: 4.6 Consensus size: 167
622715 TTAGATTTTG
* * * * * *
622725 AAAATTTCATTTCATACCTTGATGGAAGCCCGAAAAGATACAAAAAG-TTTTAAAAATCTTTTAT
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTTAT
*
622789 A-CCCTACGGATGCCCATAAGAATATAAAAGATTAAAAGGATGATTAAAATTTATTTTGGTTATG
66 ACCCCTACGGATGCCCATAAGAATATAAAAGATTAAAAAGATGATTAAAATTTATTTTGGTTATG
*
622853 AAAGTGTTAATTTAGTTATTTATTTATTTAATTTCGA
131 AAAGTGTTAATTTAATTATTTATTTATTTAATTTCGA
* * *
622890 AAAATATCATTTCATACCTTAATAGAAGCCCGAAAAGATACGAAAAGTTTTCGAAAATCTCTTAT
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTTAT
*
622955 CCCCCTACGGATGCCCATAAGAATATAAAAGATTAAAAAGATGATTAAAATTTATTTTGGTTATG
66 ACCCCTACGGATGCCCATAAGAATATAAAAGATTAAAAAGATGATTAAAATTTATTTTGGTTATG
* *
623020 AAAGTGTTAATTTAGTTATTTATTTATTTAGTTTCGA
131 AAAGTGTTAATTTAATTATTTATTTATTTAATTTCGA
*
623057 AAAATATCATTTTGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTTAT
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTTAT
* * *
623122 GCCCCTACGGATGCCCATACGAATACAAAAGATTAAAAAAGATGATTAAAATTTATTTTGGTTAT
66 ACCCCTACGGATGCCCATAAGAATATAAAAGATT-AAAAAGATGATTAAAATTTATTTTGGTTAT
* *
623187 GAAAGTGTTAATTTAATTATTTTTTTATTTAATTTCAA
130 GAAAGTGTTAATTTAATTATTTATTTATTTAATTTCGA
* * * *
623225 AAAATATTATTTCGTACCTTAATGGAAGCTCGAAAAGATACGAAAAGCTTTTGGAAATCTCTTAT
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTTAT
** *
623290 ACCTTTACGGATGCCCATAGGAATATAAAAGATTAAAAAAGATGATT-AAATTTATTTTGGTTAT
66 ACCCCTACGGATGCCCATAAGAATATAAAAGATT-AAAAAGATGATTAAAATTTATTTTGGTTAT
* *
623354 GAAAGTATTAATATAATTATTTATTTATTTAATTTCGA
130 GAAAGTGTTAATTTAATTATTTATTTATTTAATTTCGA
* * ** *
623392 AAAATATCATTTCGTACCTTAATAGAAGCCCGAAAAGATTCGAAATTTTTTTGAAAAT-TTTTAA
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTT-A
* *
623456 TACCCCTACAGATGCCCATAGGAATATAAAAGATT
65 TACCCCTACGGATGCCCATAAGAATATAAAAGATT
623491 GCAAAAATAA
Statistics
Matches: 550, Mismatches: 47, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
165 43 0.08
166 17 0.03
167 324 0.59
168 166 0.30
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (167 bp):
AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTTAT
ACCCCTACGGATGCCCATAAGAATATAAAAGATTAAAAAGATGATTAAAATTTATTTTGGTTATG
AAAGTGTTAATTTAATTATTTATTTATTTAATTTCGA
Found at i:623445 original size:335 final size:333
Alignment explanation
Indices: 622725--623490 Score: 1144
Period size: 335 Copynumber: 2.3 Consensus size: 333
622715 TTAGATTTTG
* * * * *
622725 AAAATTTCATTTCATACCTTGATGGAAGCCCGAAAAGATAC-AAAAAGTTTTAAAAATCTTTTAT
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAATTTTTGAAAATCTTTTAT
* *
622789 ACCCTACGGATGCCCATAAGAATATAAAAGATTAAAAGGATGATTAAAATTTATTTTGGTTATGA
66 CCCCTACGGATGCCCATAAGAATATAAAAGATTAAAAAGATGATTAAAATTTATTTTGGTTATGA
* *
622854 AAGTGTTAATTTAGTTATTTATTTATTTAATTTCGAAAAATATCATTTCATACCTTAATAGAAGC
131 AAGTGTTAATTTAATTATTTATTTATTTAATTTCAAAAAATATCATTTCATACCTTAATAGAAGC
*
622919 CCGAAAAGATACGAAAAGTTTTCGAAAATCTCTTATCCCCCTACGGATGCCCATAAGAATATAAA
196 CCGAAAAGATACGAAAAGTTTTCGAAAATCTCTTATACCCCTACGGATGCCCATAAGAATATAAA
* * *
622984 AGATTAAAAAGATGATTAAAATTTATTTTGGTTATGAAAGTGTTAATTTAGTTATTTATTTATTT
261 AGATTAAAAAGATGATTAAAATTTATTTTGGTTATGAAAGTATTAATATAATTATTTATTTATTT
*
623049 AGTTTCGA
326 AATTTCGA
* * *
623057 AAAATATCATTTTGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTCTTAT
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAATTTTTGAAAATCTTTTAT
* *
623122 GCCCCTACGGATGCCCATACGAATACAAAAGATTAAAAAAGATGATTAAAATTTATTTTGGTTAT
66 -CCCCTACGGATGCCCATAAGAATATAAAAGATT-AAAAAGATGATTAAAATTTATTTTGGTTAT
* * * *
623187 GAAAGTGTTAATTTAATTATTTTTTTATTTAATTTCAAAAAATATTATTTCGTACCTTAATGGAA
129 GAAAGTGTTAATTTAATTATTTATTTATTTAATTTCAAAAAATATCATTTCATACCTTAATAGAA
* * ** *
623252 GCTCGAAAAGATACGAAAAGCTTTT-GGAAATCTCTTATACCTTTACGGATGCCCATAGGAATAT
194 GCCCGAAAAGATACGAAAAG-TTTTCGAAAATCTCTTATACCCCTACGGATGCCCATAAGAATAT
623316 AAAAGATTAAAAAAGATGATT-AAATTTATTTTGGTTATGAAAGTATTAATATAATTATTTATTT
258 AAAAGATT-AAAAAGATGATTAAAATTTATTTTGGTTATGAAAGTATTAATATAATTATTTATTT
623380 ATTTAATTTCGA
322 ATTTAATTTCGA
* * **
623392 AAAATATCATTTCGTACCTTAATAGAAGCCCGAAAAGATTCGAAATTTTTTTGAAAAT-TTTTAA
1 AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAATTTTTGAAAATCTTTT-A
* *
623456 TACCCCTACAGATGCCCATAGGAATATAAAAGATT
65 T-CCCCTACGGATGCCCATAAGAATATAAAAGATT
623491 GCAAAAATAA
Statistics
Matches: 390, Mismatches: 38, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
332 37 0.09
333 19 0.05
334 33 0.08
335 285 0.73
336 16 0.04
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (333 bp):
AAAATATCATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAATTTTTGAAAATCTTTTAT
CCCCTACGGATGCCCATAAGAATATAAAAGATTAAAAAGATGATTAAAATTTATTTTGGTTATGA
AAGTGTTAATTTAATTATTTATTTATTTAATTTCAAAAAATATCATTTCATACCTTAATAGAAGC
CCGAAAAGATACGAAAAGTTTTCGAAAATCTCTTATACCCCTACGGATGCCCATAAGAATATAAA
AGATTAAAAAGATGATTAAAATTTATTTTGGTTATGAAAGTATTAATATAATTATTTATTTATTT
AATTTCGA
Found at i:624452 original size:13 final size:13
Alignment explanation
Indices: 624434--624459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
624424 TACACAAAGT
624434 ATGTATCGATACA
1 ATGTATCGATACA
624447 ATGTATCGATACA
1 ATGTATCGATACA
624460 TTGGCTTGTA
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:625640 original size:10 final size:10
Alignment explanation
Indices: 625621--625655 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
625611 GCTAGTTTGG
625621 TTTTTT-CTA
1 TTTTTTCCTA
625630 TTTTTTCCTA
1 TTTTTTCCTA
*
625640 TTTTCTCCTA
1 TTTTTTCCTA
625650 TTTTTT
1 TTTTTT
625656 TCTTGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTCCTA
Found at i:626647 original size:333 final size:330
Alignment explanation
Indices: 626244--627189 Score: 1133
Period size: 333 Copynumber: 2.9 Consensus size: 330
626234 ATTTATAGAA
* * * * *
626244 TAGAAAACTTGGT-TTTTCGAAGAAAGGAAAATTTTAAGGAAAAAATTCAAAATTCATGGAAGTG
1 TAGAAAACTTCGTATTTTCGAAAAAAGG-AAATTTCAAGGAAAAAATTCAAAATTTATGGAAATG
* * ** *
626308 AATGAATTTTTAAAAACCAAATTTTTATGAAATAAATAATAATATTTGATGAATTTTGGAAATTA
65 AATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGATGAATTTT-AAAATTA
* * * *
626373 AAAACTAAGAAAAATCCCCTCAAAAAAATTACGAAGCAGAAAACTCTATATTTCGAAAAAAAGAG
129 AAAACTAAGAAAAATCCCCTCAAAAAAATTACGGAGAAGAAAACTCTATATTTTGAAAAAAAAAG
626438 AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
194 AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* *
626503 AATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAAGCTTCCT-GAAAAAAA
259 AATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAA--TCCCTCCAAAAAAA
626567 TTAACGAAG
322 TTAACGAAG
* * * * *
626576 TAGCAAACTTTGTATTTTCAAAAAAAGGAAATTTCAAGGAAAAAAAATCAAAATTTATGGAAATA
1 TAGAAAACTTCGTATTTTCGAAAAAAGGAAATTTCAAGG-AAAAAATTCAAAATTTATGGAAATG
* * *
626641 AATGAATTTTTGAAAATTTAATTAATATAAAATAAATAATAATATTTGATGAATTTTAACAATT-
65 AATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGATGAATTTTAA-AATTA
* * * *
626705 AAAACCAAGAAAAAT-CCCTCCAAAAAAATTTGCGGAGTAGAAAACTCAATATTTTGAAAAAAAA
129 AAAACTAAGAAAAATCCCCT-CAAAAAAA-TTACGGAGAAGAAAACTCTATATTTTGAAAAAAAA
* * * *
626769 AGGAATTTTAAGGAAAAAATTCAAAATTTATGGAAATGAATGTATTTTTAAAAACTGAATTAATT
192 A-GAATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATA
* * * *
626834 TGAAATAAATAATAATATTTTGTGAATTTGAAAAATTAAAAACCATGAAAAATCCCTCCCAAAAA
256 TGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAAAAAA
* * *
626899 ATTTATGGAG
321 ATTAACGAAG
* * * *
626909 TAGAAAACTCCATATTTT-GAAAAAAGAAAAATTTCAA-GAAAAAATTCAAAATTTATGGCAATG
1 TAGAAAACTTCGTATTTTCGAAAAAAG-GAAATTTCAAGGAAAAAATTCAAAATTTATGGAAATG
* * *
626972 AATGAATTTTTGAAAACTGAATTACTATGAAATAAATAATAATATTTGATAAATTTTTAAAATTA
65 AATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGATGAA-TTTTAAAATTA
* * * * * *
627037 AAAAATAAGAAAAATTCCCCTCAAAAAATTTACGGAGAAAAAAACTTTGTATTTTG----AAATA
129 AAAACTAAGAAAAA-TCCCCTCAAAAAAATTACGGAGAAGAAAACTCTATATTTTGAAAAAAAAA
* * * * * *
627098 -AATTTCAAGGAAAAAATTCAAAAATTTATGAAAATGAATGAATTTTCGAGAATTGATTTAA-AA
193 GAATTTCAAGGAAAAAATTC-AAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATAT
* * * *
627161 GAATTAAATGATAATATTTGAGGAATTTT
257 GAAATAAATAATAATATTTTATGAATTTT
627190 GATGTTTAAA
Statistics
Matches: 524, Mismatches: 77, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
326 41 0.08
327 34 0.06
328 4 0.01
331 78 0.15
332 95 0.18
333 160 0.31
334 112 0.21
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (330 bp):
TAGAAAACTTCGTATTTTCGAAAAAAGGAAATTTCAAGGAAAAAATTCAAAATTTATGGAAATGA
ATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAATTAAA
AACTAAGAAAAATCCCCTCAAAAAAATTACGGAGAAGAAAACTCTATATTTTGAAAAAAAAAGAA
TTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAA
TAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAAAAAAATTAA
CGAAG
Found at i:626842 original size:166 final size:165
Alignment explanation
Indices: 626273--627189 Score: 1047
Period size: 165 Copynumber: 5.6 Consensus size: 165
626263 AAGAAAGGAA
* * * * ** **
626273 AATTTTAAGGAAAAAATTCAAAATTCATGGAAGTGAATGAATTTTTAAAAACCAAATTTTTATGA
1 AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* *
626338 AATAAATAATAATATTTGATGAATTTTGGAAATTAAAAACTAAGAAAAATCCC-CTCAAAAAAA-
66 AATAAATAATAATATTTGATGAATTTT-AAAATTAAAAACCAAGAAAAATCCCTC-CAAAAAAAT
* * * *
626401 TTACGAAGCAGAAAACTCTATATTTCGAAAAAAAGAG
129 TTACGGAGTAGAAAACTCTATATTTTGAAAAAAAAAG
626438 AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
1 AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* * *
626503 AATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAAGCTTCCT-GAAAAAAA
66 AATAAATAATAATATTTGATGAATTTT-AAAATTAAAAACCAAGAAAAA--TCCCTCCAAAAAAA
* * * * * * *
626567 TTAACGAAGTAGCAAACTTTGTATTTT-CAAAAAAAGG
128 TTTACGGAGTAGAAAACTCTATATTTTGAAAAAAAAAG
* * * *
626604 AAATTTCAAGGAAAAAAAATCAAAATTTATGGAAATAAATGAATTTTTGAAAATTTAATTAATAT
1 -AATTTCAAGG-AAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATAT
*
626669 AAAATAAATAATAATATTTGATGAATTTTAACAATT-AAAACCAAGAAAAATCCCTCCAAAAAAA
64 GAAATAAATAATAATATTTGATGAATTTTAA-AATTAAAAACCAAGAAAAATCCCTCCAAAAAAA
* *
626733 TTTGCGGAGTAGAAAACTCAATATTTTGAAAAAAAAAGG
128 TTTACGGAGTAGAAAACTCTATATTTTGAAAAAAAAA-G
* * * *
626772 AATTTTAAGGAAAAAATTCAAAATTTATGGAAATGAATGTATTTTTAAAAACTGAATTAATTTGA
1 AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* * *
626837 AATAAATAATAATATTTTG-TGAATTTGAAAAATTAAAAACCATGAAAAATCCCTCCCAAAAAAT
66 AATAAATAATAATA-TTTGATGAATTT-TAAAATTAAAAACCAAGAAAAATCCCTCCAAAAAAAT
* *
626901 TTATGGAGTAGAAAACTCCATATTTTGAAAAAAGAAA-
129 TTACGGAGTAGAAAACTCTATATTTTGAAAAAA-AAAG
* *
626938 AATTTCAA-GAAAAAATTCAAAATTTATGGCAATGAATGAATTTTTGAAAACTGAATTACTATGA
1 AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* **
627002 AATAAATAATAATATTTGATAAATTTTTAAAATTAAAAAATAAGAAAAATTCCC-CTC-AAAAAA
66 AATAAATAATAATATTTGATGAA-TTTTAAAATTAAAAACCAAGAAAAA-TCCCTC-CAAAAAAA
* * * * *
627065 TTTACGGAGAAAAAAACTTTGTATTTTG----AAATA-
128 TTTACGGAGTAGAAAACTCTATATTTTGAAAAAAAAAG
* * * * * *
627098 AATTTCAAGGAAAAAATTCAAAAATTTATGAAAATGAATGAATTTTCGAGAATTGATTTAA-AAG
1 AATTTCAAGGAAAAAATTC-AAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATG
* * *
627162 AATTAAATGATAATATTTGAGGAATTTT
65 AAATAAATAATAATATTTGATGAATTTT
627190 GATGTTTAAA
Statistics
Matches: 647, Mismatches: 85, Indels: 45
0.83 0.11 0.06
Matches are distributed among these distances:
160 14 0.02
161 34 0.05
162 34 0.05
164 4 0.01
165 221 0.34
166 128 0.20
167 128 0.20
168 84 0.13
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (165 bp):
AATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGA
AATAAATAATAATATTTGATGAATTTTAAAATTAAAAACCAAGAAAAATCCCTCCAAAAAAATTT
ACGGAGTAGAAAACTCTATATTTTGAAAAAAAAAG
Found at i:630269 original size:52 final size:52
Alignment explanation
Indices: 630182--630286 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
630172 AATCTTTTTT
* *
630182 TCACTGTTCATCACTGTTCATGTATCGATATATTGTGAATAGTATCGATACA
1 TCACTGTTCATCACTATTCATGTATCGATACATTGTGAATAGTATCGATACA
* *
630234 TCACTGTTCATTACTATTCATGTATTGATACATTGTGAATAGTATCGATACA
1 TCACTGTTCATCACTATTCATGTATCGATACATTGTGAATAGTATCGATACA
630286 T
1 T
630287 TGAGTCCAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (52 bp):
TCACTGTTCATCACTATTCATGTATCGATACATTGTGAATAGTATCGATACA
Found at i:636493 original size:20 final size:21
Alignment explanation
Indices: 636461--636507 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
636451 GAAGGTGCTG
636461 AACATGCTGT-AAATGCATGA
1 AACATGCTGTAAAATGCATGA
636481 AACATAGCT-TAAAATGCATGA
1 AACAT-GCTGTAAAATGCATGA
*
636502 ATCATG
1 AACATG
636508 GGCTGTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (21 bp):
AACATGCTGTAAAATGCATGA
Found at i:637408 original size:13 final size:13
Alignment explanation
Indices: 637390--637445 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
637380 TCTAGGATTT
637390 TATCGATACAATG
1 TATCGATACAATG
637403 TATCGATACAA--
1 TATCGATACAATG
637414 -A--GAT-CAATG
1 TATCGATACAATG
637423 TATCGATACAATG
1 TATCGATACAATG
637436 TATCGATACA
1 TATCGATACA
637446 TTGAATAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
10 2 0.05
12 3 0.08
13 26 0.70
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (13 bp):
TATCGATACAATG
Done.