Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 18 of 144
Found at i:5088745 original size:22 final size:23
Alignment explanation
Indices: 5088702--5088759 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 23
5088692 TCAAAAAATA
*
5088702 TTAAAAATATTTTTATATAATTT
1 TTAAAAATAATTTTATATAATTT
5088725 TTAAAAATAAATTTT-TA-AATTT
1 TTAAAAAT-AATTTTATATAATTT
5088747 TTAAAAATGAATT
1 TTAAAAAT-AATT
5088760 AAATGCTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 17 0.53
23 10 0.31
24 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAAAAATAATTTTATATAATTT
Found at i:5094186 original size:24 final size:24
Alignment explanation
Indices: 5094159--5094206 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5094149 TATATATATA
*
5094159 TATTA-GTAATAAAATGTTTGATTC
1 TATTATGTAACAAAAT-TTTGATTC
*
5094183 TATTATTTAACAAAATTTTGATTC
1 TATTATGTAACAAAATTTTGATTC
5094207 AAAAACATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (24 bp):
TATTATGTAACAAAATTTTGATTC
Found at i:5110780 original size:17 final size:16
Alignment explanation
Indices: 5110735--5110810 Score: 53
Period size: 19 Copynumber: 4.2 Consensus size: 16
5110725 ATATACGTGT
5110735 ATATATATGAATAAAAAA
1 ATATATAT-AA-AAAAAA
*
5110753 ATTTACTTATAAAAAATAA
1 ATATA--TATAAAAAA-AA
*
5110772 ATATGTATATAAAAACAAC
1 ATA--TATATAAAAA-AAA
5110791 ATATATATAAATAAAAA
1 ATATATATAAA-AAAAA
5110808 ATA
1 ATA
5110811 ATTACAGATA
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
17 13 0.28
18 10 0.21
19 18 0.38
20 4 0.09
21 2 0.04
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (16 bp):
ATATATATAAAAAAAA
Found at i:5110794 original size:19 final size:17
Alignment explanation
Indices: 5110760--5110810 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
5110750 AAAATTTACT
* *
5110760 TATAAAAAATAAATATG
1 TATAAAAAACAAATATA
5110777 TATATAAAAACAACATATA
1 TATA-AAAAACAA-ATATA
5110796 TATAAATAAA-AAATA
1 TATAAA-AAACAAATA
5110811 ATTACAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 7 0.24
18 11 0.38
19 11 0.38
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (17 bp):
TATAAAAAACAAATATA
Found at i:5116250 original size:16 final size:18
Alignment explanation
Indices: 5116196--5116250 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
5116186 TGCAATATTC
5116196 TTTTATTTTA--TAAATAA
1 TTTTATTTTATTTAAAT-A
5116213 CTTTCTATTTTATTTAAATA
1 -TTT-TATTTTATTTAAATA
5116233 TTTTATTTT-TTT-AATA
1 TTTTATTTTATTTAAATA
5116249 TT
1 TT
5116251 ATACTACACC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 9 0.26
19 10 0.29
20 1 0.03
21 5 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTTTATTTAAATA
Found at i:5117041 original size:16 final size:18
Alignment explanation
Indices: 5117010--5117047 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5117000 TATTTTCATT
5117010 ATTTTAAAAATTA-TTTA
1 ATTTTAAAAATTATTTTA
*
5117027 ATTTT-AAATTTATTTTA
1 ATTTTAAAAATTATTTTA
5117044 ATTT
1 ATTT
5117048 ACATACTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAAAAATTATTTTA
Found at i:5120612 original size:51 final size:51
Alignment explanation
Indices: 5120536--5120634 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
5120526 AAAGTACAAC
5120536 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
1 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
*
5120587 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAATTATTAGGGAT
1 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGAT
5120635 TGGAAGTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (51 bp):
CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
Found at i:5121539 original size:14 final size:14
Alignment explanation
Indices: 5121520--5121559 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5121510 TTGATTGCCA
5121520 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5121534 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5121548 GGAAAATGTTTT
1 GTAAAATGTTTT
5121560 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5121568 original size:20 final size:20
Alignment explanation
Indices: 5121543--5121582 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5121533 CGTAAAATGA
*
5121543 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
5121563 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
5121583 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5121572 original size:34 final size:35
Alignment explanation
Indices: 5121528--5121594 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5121518 CAGTAAAATG
*
5121528 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
5121562 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
5121595 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:5121598 original size:14 final size:15
Alignment explanation
Indices: 5121522--5121598 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
5121512 GATTGCCAGT
* *
5121522 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
5121536 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
5121550 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
5121570 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
5121585 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
5121599 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:5123203 original size:12 final size:12
Alignment explanation
Indices: 5123186--5123211 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5123176 TTTTCCAGAA
5123186 AACATTATATCG
1 AACATTATATCG
5123198 AACATTATATCG
1 AACATTATATCG
5123210 AA
1 AA
5123212 TACACAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AACATTATATCG
Found at i:5125796 original size:18 final size:18
Alignment explanation
Indices: 5125775--5125825 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
5125765 AGGAATGAAG
5125775 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** *
5125793 GAAGGGAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
5125811 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
5125826 CCTGAGAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:5130329 original size:17 final size:18
Alignment explanation
Indices: 5130303--5130336 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5130293 TAACAAGAGT
*
5130303 TTAATTTAAA-TTATTTG
1 TTAATATAAACTTATTTG
5130320 TTAATATAAACTTATTT
1 TTAATATAAACTTATTT
5130337 AATTTGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTAATATAAACTTATTTG
Found at i:5138458 original size:7 final size:7
Alignment explanation
Indices: 5138446--5138470 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5138436 TTTATTAATT
5138446 AAAAATA
1 AAAAATA
5138453 AAAAATA
1 AAAAATA
5138460 AAAAATA
1 AAAAATA
5138467 AAAA
1 AAAA
5138471 TATGCTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:5148685 original size:77 final size:77
Alignment explanation
Indices: 5148521--5148769 Score: 221
Period size: 77 Copynumber: 3.2 Consensus size: 77
5148511 CATAGAACGT
* * * *
5148521 GATATTAAATCAAGCGAATTGTTTGGATATCAAAGGTCGCAATCTTAAATCAAGCGAACCATAAA
1 GATATTAAATCAAGCGAACTGTTAGAATATCAAAGGTCGCAATCTTAAATCAAGCAAACCATAAA
*
5148586 AATGACAGTCGC
66 AATGACAGTCAC
* * * * * *
5148598 GATATCAAATCAAGCAAACTGTTAGAATATCGAAGGTTGCGATCTTAAATCAAGTAAACCATAAA
1 GATATTAAATCAAGCGAACTGTTAGAATATCAAAGGTCGCAATCTTAAATCAAGCAAACCATAAA
** * *
5148663 AATGTTATTCAT
66 AATGACAGTCAC
* * * * * * * * * ** *
5148675 GTTGTTAAATCAAGCGAACTGTTAGAAGACCGAATGCCGCAATTTTAAACCAAGTGAACCGTAAA
1 GATATTAAATCAAGCGAACTGTTAGAATATCAAAGGTCGCAATCTTAAATCAAGCAAACCATAAA
5148740 AATGACAG-CTAC
66 AATGACAGTC-AC
* *
5148752 GATCTTCAATCAAGCGAA
1 GATATTAAATCAAGCGAA
5148770 ATGTAAAAAT
Statistics
Matches: 135, Mismatches: 36, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
76 1 0.01
77 134 0.99
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (77 bp):
GATATTAAATCAAGCGAACTGTTAGAATATCAAAGGTCGCAATCTTAAATCAAGCAAACCATAAA
AATGACAGTCAC
Found at i:5149882 original size:23 final size:22
Alignment explanation
Indices: 5149825--5149882 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
5149815 TTTTAATTTA
*
5149825 CTTAATTTT-CGTTGTATTTTG
1 CTTAATTTTGCGTCGTATTTTG
*
5149846 CTTAATTGTAGCGTCGTATTTTG
1 CTTAATT-TTGCGTCGTATTTTG
5149869 CTTAATTTTCGCGT
1 CTTAATTTT-GCGT
5149883 TTGAATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 7 0.23
22 2 0.06
23 22 0.71
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (22 bp):
CTTAATTTTGCGTCGTATTTTG
Found at i:5151551 original size:11 final size:11
Alignment explanation
Indices: 5151535--5151559 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5151525 TTGAAGTAAG
5151535 TAAAAATCCAA
1 TAAAAATCCAA
5151546 TAAAAATCCAA
1 TAAAAATCCAA
5151557 TAA
1 TAA
5151560 TTTTAACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAAATCCAA
Found at i:5159648 original size:21 final size:22
Alignment explanation
Indices: 5159624--5159676 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
5159614 TTTTAATTTA
5159624 CTTAATTTTCG-TTGTATTTTG
1 CTTAATTTTCGATTGTATTTTG
5159645 CTTAATTTTCGCATTGTATTTTG
1 CTTAATTTTCG-ATTGTATTTTG
*
5159668 ATTAATTTT
1 CTTAATTTT
5159677 GGCGTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 11 0.38
23 18 0.62
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.60
Consensus pattern (22 bp):
CTTAATTTTCGATTGTATTTTG
Found at i:5175539 original size:39 final size:39
Alignment explanation
Indices: 5175490--5175564 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5175480 ACAGGTGTCA
*
5175490 TGTGACCAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
* *
5175529 TGTGAACAGGCTGGGTCAAGTTTTTCTGGTTCAAAT
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAAT
5175565 CCATCCAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (39 bp):
TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
Found at i:5181151 original size:3 final size:3
Alignment explanation
Indices: 5181136--5181186 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
5181126 AGTAAATGAC
* * *
5181136 AAT AAT GAT AAT AAT AAT AAT AAT AACT AATT AGT TA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT AAT
5181182 AAT AA
1 AAT AA
5181187 AAAGGGACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 1 0.03
3 33 0.85
4 5 0.13
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5188666 original size:37 final size:40
Alignment explanation
Indices: 5188607--5188741 Score: 125
Period size: 41 Copynumber: 3.4 Consensus size: 40
5188597 AACTTCAAGT
* *
5188607 CGATGAGGCACTGGGTGCCAATTTA-T-TTCGG-TTTAAC
1 CGATGAGACACTGGGTGTCAATTTACTATTCGGATTTAAC
* * **
5188644 CGATGAGACACTGAGTGTCAATTTACTACTTTGGATTTATT
1 CGATGAGACACTGGGTGTCAATTTACTA-TTCGGATTTAAC
* * *
5188685 CGATGAGACACTGGGTGTTAATTTACTACTTC-GAATTATC
1 CGATGAGACACTGGGTGTCAATTTACTA-TTCGGATTTAAC
* *
5188725 CAATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5188742 CCAAATTGGT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
37 22 0.27
38 1 0.01
40 25 0.31
41 33 0.41
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTACTATTCGGATTTAAC
Found at i:5199644 original size:74 final size:75
Alignment explanation
Indices: 5199555--5199698 Score: 254
Period size: 74 Copynumber: 1.9 Consensus size: 75
5199545 AGGTTTAGGA
* * *
5199555 ACTAAATTGAATAAAAGTAAAATTTTTAGGGTAATTTTGTAAAAATG-GAAAAATGACGAAATTT
1 ACTAAATTGAATAAAAGTAAAATTTTTAGGGCAATTTTGTAAAAATGAAAAAAATGACAAAATTT
5199619 CAAGACAGGG
66 CAAGACAGGG
5199629 ACTAAATTGAATAAAAGTAAAATTTTTAGGGCAATTTTGTAAAAATGAAAAAAATGACAAAATTT
1 ACTAAATTGAATAAAAGTAAAATTTTTAGGGCAATTTTGTAAAAATGAAAAAAATGACAAAATTT
5199694 CAAGA
66 CAAGA
5199699 ATTGAATAGT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
74 46 0.70
75 20 0.30
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (75 bp):
ACTAAATTGAATAAAAGTAAAATTTTTAGGGCAATTTTGTAAAAATGAAAAAAATGACAAAATTT
CAAGACAGGG
Found at i:5203859 original size:15 final size:15
Alignment explanation
Indices: 5203839--5203871 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5203829 TTTGCCATAA
5203839 TGTCATAACATGCTC
1 TGTCATAACATGCTC
5203854 TGTCATAACATGCTC
1 TGTCATAACATGCTC
5203869 TGT
1 TGT
5203872 TAGAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (15 bp):
TGTCATAACATGCTC
Found at i:5204587 original size:15 final size:15
Alignment explanation
Indices: 5204567--5204597 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5204557 AGGTTTTTGC
5204567 ATCTCAGAGGTCTAT
1 ATCTCAGAGGTCTAT
5204582 ATCTCAGAGGTCTAT
1 ATCTCAGAGGTCTAT
5204597 A
1 A
5204598 GCTTGTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (15 bp):
ATCTCAGAGGTCTAT
Found at i:5216426 original size:15 final size:15
Alignment explanation
Indices: 5216406--5216436 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5216396 CTATCATCTT
5216406 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
5216421 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
5216436 T
1 T
5216437 TACAACGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:5216470 original size:20 final size:20
Alignment explanation
Indices: 5216445--5216486 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5216435 CTTACAACGG
*
5216445 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
5216465 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
5216485 TA
1 TA
5216487 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:5219887 original size:18 final size:18
Alignment explanation
Indices: 5219854--5219888 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5219844 ACCAGCAGAT
* *
5219854 GGCATACTGACTTGTTGG
1 GGCATACTAACCTGTTGG
5219872 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
5219889 TGGAGAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGG
Found at i:5221151 original size:15 final size:15
Alignment explanation
Indices: 5221131--5221161 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5221121 CTATCATCTT
*
5221131 TAACTGCTAATAGAC
1 TAACTGCTAACAGAC
5221146 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
5221161 T
1 T
5221162 TACAACGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:5221195 original size:20 final size:20
Alignment explanation
Indices: 5221170--5221211 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5221160 CTTACAACGG
*
5221170 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
5221190 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
5221210 TA
1 TA
5221212 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:5228618 original size:3 final size:3
Alignment explanation
Indices: 5228612--5228667 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
5228602 AGGAGGAGAG
5228612 GAA GAA GGAA -AA GAA GAA GAA GAA GAA GAA GAA GAA GACA GAGA GAA
1 GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GA-A GAA
*
5228659 -AT GAA GAA G
1 GAA GAA GAA G
5228668 GGGATAAAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.07
3 34 0.74
4 9 0.20
ACGTcount: A:0.62, C:0.02, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:5228620 original size:12 final size:12
Alignment explanation
Indices: 5228605--5228649 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
5228595 GAGGAGGAGG
*
5228605 AGGAGAGGAAGA
1 AGGAGAAGAAGA
*
5228617 AGGAAAAGAAGA
1 AGGAGAAGAAGA
*
5228629 AGAAGAAGAAGA
1 AGGAGAAGAAGA
*
5228641 AGAAGAAGA
1 AGGAGAAGA
5228650 CAGAGAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
AGGAGAAGAAGA
Found at i:5234255 original size:44 final size:44
Alignment explanation
Indices: 5234198--5234281 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
5234188 AACCTTCCTT
* *
5234198 TTTATCTTTTAACAAAAATCACTTGCAACGTAAATTAACTACTC
1 TTTATCTTCTAACAAAAATCACTTACAACGTAAATTAACTACTC
5234242 TTTATCTTCTAACAAAAATCACTTACAACGTAAATTAACT
1 TTTATCTTCTAACAAAAATCACTTACAACGTAAATTAACT
5234282 TTCTTTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (44 bp):
TTTATCTTCTAACAAAAATCACTTACAACGTAAATTAACTACTC
Found at i:5235625 original size:87 final size:87
Alignment explanation
Indices: 5235476--5235960 Score: 355
Period size: 87 Copynumber: 5.6 Consensus size: 87
5235466 TAAGATTTTT
* * * *
5235476 TTTTCATTATTAAT-AGCACTATT--AAAAA--GAGGTAAAGTAGTTTTATTTAATACCTAACAA
1 TTTT-ATTATTAATGA-CACTATTAAAAAAAGTGAAGTAACGTAATTTTATTTAATACCTAAAAA
*
5235536 GTTTTTTTTATGTTTGGAAACGTA
64 GTTTTTTTTATGTTTGGAAATGTA
* *
5235560 TTTTATTATTAATGACACTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATAACTAAAAAGT
1 TTTTATTATTAATGACACTATTAAAAAAAGTGAAGTAACGTAATTTTATTTAATACCTAAAAAGT
5235625 TTTTTTTATGTTTGGAAATGTA
66 TTTTTTTATGTTTGGAAATGTA
* * * * ***
5235647 TTTCATTATTAATGACACTATTTAAAAAAAAGTGAAGTAACATAAAAATTAGTTTTTTGTATGTT
1 TTTTATTATTAATGACACTA-TT-AAAAAAAGTGAAGTAACGT---AATT--TTATTT-AATACC
** * * *
5235712 TGGAAA-TGTATTCTAT-TATT---AATG-A
58 TAAAAAGTTTTTTTTATGT-TTGGAAATGTA
* * * * *
5235737 ---CACTGTTAA-G--A--A--AAAAAAGGTAAAGTAACGTAATTTTATTTAATACCTAAAAAGT
1 TTTTATTATTAATGACACTATTAAAAAAAGTGAAGTAACGTAATTTTATTTAATACCTAAAAAG-
5235792 TTTTTTTTTTTTTATGTTTGGAAATGTA
65 -----TTTTTTTTATGTTTGGAAATGTA
* * * * * * * *
5235820 TTCTATTATTAATCACATTAATAAAAAATGGTGGAGTAACGTAATTTTATTTAATACCTACAATG
1 TTTTATTATTAATGACACTATTAAAAAA-AGTGAAGTAACGTAATTTTATTTAATACCTAAAAAG
5235885 TTTTTTTTTATGTTTGGAAATGTA
65 -TTTTTTTTATGTTTGGAAATGTA
*
5235909 TTTTATTATTAATGACACTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTA
1 TTTTATTATTAATGACACTATTAAAAAAAGTGAAGTAACGTAATTTTATTTA
5235961 TCTTTGGAAA
Statistics
Matches: 316, Mismatches: 48, Indels: 70
0.73 0.11 0.16
Matches are distributed among these distances:
72 6 0.02
73 5 0.02
75 4 0.01
78 16 0.05
79 9 0.03
80 1 0.00
82 5 0.02
83 17 0.05
84 6 0.02
85 5 0.02
86 7 0.02
87 77 0.24
88 23 0.07
89 67 0.21
90 1 0.00
91 5 0.02
92 3 0.01
93 7 0.02
94 46 0.15
95 6 0.02
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (87 bp):
TTTTATTATTAATGACACTATTAAAAAAAGTGAAGTAACGTAATTTTATTTAATACCTAAAAAGT
TTTTTTTATGTTTGGAAATGTA
Found at i:5235935 original size:89 final size:90
Alignment explanation
Indices: 5235689--5235960 Score: 325
Period size: 89 Copynumber: 2.9 Consensus size: 90
5235679 TGAAGTAACA
* *
5235689 TAAAAATTAG-TTTTTTGTATGTTTGGAAATGTATTCTATTATTAATGACACTGTTAAGAAAAAA
1 TAAAAATT-GTTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATT-----AAAA
*
5235753 AAGGTAAAGTAACGTAATTTTATTTAATACC
60 AAGGTGAAGTAACGTAATTTTATTTAATACC
* * * *
5235784 TAAAAAGTTTTTTTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATCACATTAATAAAAAAT
1 TAAAAA---TTGTTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAA-
*
5235849 GGTGGAGTAACGTAATTTTATTTAATACC
62 GGTGAAGTAACGTAATTTTATTTAATACC
* * *
5235878 T-ACAA-TGTTTTTTTTTATGTTTGGAAATGTATTTTATTATTAATGACACTATTAAAAAAAGTG
1 TAAAAATTGTTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAGGTG
*
5235941 AAGTAACGTAGTTTTATTTA
66 AAGTAACGTAATTTTATTTA
5235961 TCTTTGGAAA
Statistics
Matches: 155, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
88 21 0.14
89 49 0.32
93 9 0.06
94 28 0.18
95 6 0.04
98 42 0.27
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (90 bp):
TAAAAATTGTTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAGGTG
AAGTAACGTAATTTTATTTAATACC
Found at i:5243673 original size:14 final size:15
Alignment explanation
Indices: 5243654--5243686 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5243644 TTTATTTACT
*
5243654 AAAATAATACA-AAA
1 AAAATAAAACAGAAA
5243668 AAAATAAAACAGAAA
1 AAAATAAAACAGAAA
5243683 AAAA
1 AAAA
5243687 AAGCTACGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAATAAAACAGAAA
Found at i:5243859 original size:10 final size:10
Alignment explanation
Indices: 5243846--5243961 Score: 51
Period size: 10 Copynumber: 11.3 Consensus size: 10
5243836 GAGAAGAAAG
5243846 AAAGAAAGAA
1 AAAGAAAGAA
5243856 AAAGAAAGAA
1 AAAGAAAGAA
* *
5243866 AAGGAGAGGAGAGG
1 AA--AGA-AAGA-A
5243880 AAAGAAAGAA
1 AAAGAAAGAA
*
5243890 AAAGAAGGAA
1 AAAGAAAGAA
* *
5243900 AGA-AAAG-G
1 AAAGAAAGAA
*
5243908 AAGGAGAAGAA
1 AAAGA-AAGAA
5243919 AAA-AAA-AA
1 AAAGAAAGAA
**
5243927 GAAAGAAGAGGG
1 -AAAGAA-AGAA
* *
5243939 AAGGAAGGAA
1 AAAGAAAGAA
5243949 AAAGAAAGAA
1 AAAGAAAGAA
5243959 AAA
1 AAA
5243962 AAGGTGATCT
Statistics
Matches: 75, Mismatches: 20, Indels: 22
0.64 0.17 0.19
Matches are distributed among these distances:
8 3 0.04
9 9 0.12
10 41 0.55
11 11 0.15
12 6 0.08
13 3 0.04
14 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:5243885 original size:30 final size:30
Alignment explanation
Indices: 5243849--5243957 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 30
5243839 AAGAAAGAAA
*
5243849 GAAAGAAAAAGAAAGA-AAAGGAGAGGAGAG
1 GAAAGAAAAA-AAAGAGAAAGAAGAGGAGAG
*
5243879 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGA-AG
1 GAAAGAAA-AAAAAG-A-GAAAGAAGAGGAGAG
*
5243911 GAGAAGAAAAAAAAAAGAAAGAAGAGG-GAAG
1 GA-AAGAAAAAAAAGAGAAAGAAGAGGAG-AG
*
5243942 GAAGGAAAAAGAAAGA
1 GAAAGAAAAA-AAAGA
5243958 AAAAAAGGTG
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
30 29 0.45
31 12 0.18
32 9 0.14
33 15 0.23
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (30 bp):
GAAAGAAAAAAAAGAGAAAGAAGAGGAGAG
Found at i:5243885 original size:38 final size:37
Alignment explanation
Indices: 5243833--5243935 Score: 138
Period size: 38 Copynumber: 2.8 Consensus size: 37
5243823 AGGAGAGGGA
5243833 AAGGAGAAGAAAGAAAGAAAGAAAAAGAAAGAAAAGG
1 AAGGAGAAGAAAGAAAGAAAGAAAAAGAAAGAAAAGG
* *
5243870 AGAGGAGAGGAAAGAAAGAAA-AAGAAGGAAAGAAAAGG
1 A-AGGAGAAGAAAGAAAGAAAGAA-AAAGAAAGAAAAGG
*
5243908 AAGGAGAAGAAA-AAAAAAAGAAAGAAGA
1 AAGGAGAAGAAAGAAAGAAAGAAA-AAGA
5243936 GGGAAGGAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
36 7 0.12
37 18 0.32
38 32 0.56
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (37 bp):
AAGGAGAAGAAAGAAAGAAAGAAAAAGAAAGAAAAGG
Found at i:5243961 original size:38 final size:36
Alignment explanation
Indices: 5243842--5243963 Score: 114
Period size: 38 Copynumber: 3.4 Consensus size: 36
5243832 AAAGGAGAAG
*
5243842 AAAGAAAGAAAGAAAAAGAAAGAAAAGGAGAGGAGAGG-
1 AAAGAAAGAAA-AAAAAGAAAGAAAGGGA-AGGA-AGGA
*
5243880 AAAGAAAGAAAAAGAAGGAAAG-AA---AAGGAAGGA
1 AAAGAAAGAAAAA-AAAGAAAGAAAGGGAAGGAAGGA
*
5243913 GAAG-AA-AAAAAAAAGAAAGAAGAGGGAAGGAAGGAA
1 AAAGAAAGAAAAAAAAGAAAGAA-AGGGAAGGAAGG-A
5243949 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
5243964 GGTGATCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 20
0.74 0.04 0.21
Matches are distributed among these distances:
30 7 0.10
31 6 0.09
32 6 0.09
33 7 0.10
34 1 0.01
35 8 0.11
36 4 0.06
37 6 0.09
38 25 0.36
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (36 bp):
AAAGAAAGAAAAAAAAGAAAGAAAGGGAAGGAAGGA
Found at i:5246223 original size:12 final size:12
Alignment explanation
Indices: 5246208--5246238 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5246198 ACAAGTCCCG
5246208 AGCCAGAACCCC
1 AGCCAGAACCCC
*
5246220 AGCCAGAGCCCC
1 AGCCAGAACCCC
5246232 AGCCAGA
1 AGCCAGA
5246239 TCCCGAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.45, G:0.23, T:0.00
Consensus pattern (12 bp):
AGCCAGAACCCC
Found at i:5251992 original size:25 final size:22
Alignment explanation
Indices: 5251959--5252020 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 22
5251949 GAAGAATATG
*
5251959 AGAAAGAAAAATAAATGAGAAGA
1 AGAAGGAAAAATAAATGA-AAGA
*
5251982 AGAAAAGG-AAAATAAA-GAAATA
1 AG--AAGGAAAAATAAATGAAAGA
5252004 AGAAGGAAAAACTAAAT
1 AGAAGGAAAAA-TAAAT
5252021 TGTTCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
20 4 0.12
21 4 0.12
22 9 0.28
23 4 0.12
24 8 0.25
25 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (22 bp):
AGAAGGAAAAATAAATGAAAGA
Found at i:5271745 original size:18 final size:20
Alignment explanation
Indices: 5271707--5271766 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
5271697 TCAAAAAACA
*
5271707 AAAATATTTTTATATTTTTT
1 AAAATAATTTTATATTTTTT
*
5271727 AAAATAATTTTA-ATTTTTA
1 AAAATAATTTTATATTTTTT
*
5271746 AAAATAAATTTCATAATTTTT
1 AAAAT-AATTTTAT-ATTTTT
5271767 GAGCATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.32
20 17 0.50
22 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAATAATTTTATATTTTTT
Found at i:5278337 original size:38 final size:38
Alignment explanation
Indices: 5278286--5278364 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
5278276 ATACTTTACA
5278286 GTATATATAAGGGATCATTCCTTGTCTTGTAGTGTCAC
1 GTATATATAAGGGATCATTCCTTGTCTTGTAGTGTCAC
5278324 GTATATATAAGGGATCATTCCTTGTCTTGTAGTGTCAC
1 GTATATATAAGGGATCATTCCTTGTCTTGTAGTGTCAC
5278362 GTA
1 GTA
5278365 ATTGACAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (38 bp):
GTATATATAAGGGATCATTCCTTGTCTTGTAGTGTCAC
Found at i:5281793 original size:54 final size:54
Alignment explanation
Indices: 5281735--5281844 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
5281725 TTACACGATA
5281735 TAGACAACTCCAAAAAAATAAAATATTATATTAACTTATCAATTAAAATAATCT
1 TAGACAACTCCAAAAAAATAAAATATTATATTAACTTATCAATTAAAATAATCT
5281789 TAGACAACTCCAAAAAAATAAAATATTATATTAACTTATCAATTAAAATAATCT
1 TAGACAACTCCAAAAAAATAAAATATTATATTAACTTATCAATTAAAATAATCT
5281843 TA
1 TA
5281845 CATTTCTCTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.32
Consensus pattern (54 bp):
TAGACAACTCCAAAAAAATAAAATATTATATTAACTTATCAATTAAAATAATCT
Found at i:5282002 original size:6 final size:6
Alignment explanation
Indices: 5281991--5282024 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5281981 AACTTTACTT
5281991 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAA
5282025 TTTAGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:5286156 original size:69 final size:69
Alignment explanation
Indices: 5286078--5286232 Score: 197
Period size: 69 Copynumber: 2.2 Consensus size: 69
5286068 GAAATTATAA
* * * *
5286078 ACGTAAGACCATAGTGAGACTATGGCCGTTGTTTGGATA-TAAGACCATGGTTGGACCATGGCAA
1 ACGTAAGACCATAGCGAGACTATGGCAGTTATTT--ATACAAAGACCATGGTTGGACCATGGCAA
5286142 TG-TAT
64 TGATAT
* *
5286147 ACGTAAGACCATAGCGAGGCTATGGTAGTTATTTATACGAAAGACCATGGTTGGACCATGGCAAT
1 ACGTAAGACCATAGCGAGACTATGGCAGTTATTTATAC-AAAGACCATGGTTGGACCATGGCAAT
5286212 GTATAT
65 G-ATAT
*
5286218 ATGTAAGACCATAGC
1 ACGTAAGACCATAGC
5286233 TGGGTTATGG
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
67 3 0.04
69 55 0.73
71 17 0.23
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (69 bp):
ACGTAAGACCATAGCGAGACTATGGCAGTTATTTATACAAAGACCATGGTTGGACCATGGCAATG
ATAT
Found at i:5293579 original size:50 final size:50
Alignment explanation
Indices: 5293408--5293695 Score: 220
Period size: 49 Copynumber: 5.7 Consensus size: 50
5293398 GATAATAACA
* * * * ** * * *
5293408 TGCCAAAGCCATGTCCCAGATATAGTCTTACATGGAATATTTCATGT-GC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ** * * *
5293457 TACCAATGCCATGTCCCAGACATAGTCTTACATGGGATGTTTCATGT-GC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * **
5293506 TACCGATGCCATGTTCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * **
5293556 TGCCAACGCCATGTCCCAAACATGGTCTTATATGGGACATTTTGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5293606 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
5293661 ATGCCAATGCCATGTCCTATACATGGTCTTACATG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATG
5293696 AGATCTCTTT
Statistics
Matches: 193, Mismatches: 39, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
49 82 0.42
50 74 0.38
53 4 0.02
55 2 0.01
56 31 0.16
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5303725 original size:15 final size:14
Alignment explanation
Indices: 5303707--5303753 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5303697 ATAATAATTA
5303707 AAATAATAAGAAAAT
1 AAATAATAA-AAAAT
*
5303722 AAATAA-AAACAA-
1 AAATAATAAAAAAT
*
5303734 AAATAATAAAAATT
1 AAATAATAAAAAAT
5303748 AAATAA
1 AAATAA
5303754 AATGAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 6 0.22
13 7 0.26
14 8 0.30
15 6 0.22
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATAATAAAAAAT
Found at i:5303755 original size:10 final size:10
Alignment explanation
Indices: 5303742--5303771 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5303732 AAAAATAATA
*
5303742 AAAATTAAAT
1 AAAATGAAAT
5303752 AAAATGAAAT
1 AAAATGAAAT
5303762 AAAATGAAAT
1 AAAATGAAAT
5303772 GAAAGAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAATGAAAT
Found at i:5305418 original size:17 final size:17
Alignment explanation
Indices: 5305396--5305428 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5305386 TTTGAATTAG
5305396 TGAATTTTGTGATTTAT
1 TGAATTTTGTGATTTAT
5305413 TGAATTTTGTGATTTA
1 TGAATTTTGTGATTTA
5305429 AAAAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (17 bp):
TGAATTTTGTGATTTAT
Found at i:5306720 original size:46 final size:46
Alignment explanation
Indices: 5306650--5306788 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
5306640 CATGGCAAAG
*
5306650 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
5306696 TGTGAAAAGTGGGTATGGTGTTTCAGTGAAGAAAACCATACTGACT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
5306742 TGTGAAAAGTAGGTATGGTATTTCTGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
5306788 T
1 T
5306789 ATAGCAATGT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:5312404 original size:13 final size:13
Alignment explanation
Indices: 5312381--5312414 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
5312371 AAAACCATAT
5312381 ATTTT-AATTTAA
1 ATTTTAAATTTAA
5312393 ATTTTAAATTTAA
1 ATTTTAAATTTAA
5312406 ATTGTTAAA
1 ATT-TTAAA
5312415 AGATTAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTTTAAATTTAA
Found at i:5313908 original size:24 final size:24
Alignment explanation
Indices: 5313871--5313957 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
5313861 GGACACACCA
*
5313871 CAACTCGTATGAGCTTATCGATTT
1 CAACTCGTATGAGCTTACCGATTT
5313895 CAACTCGTGA-GAGCTTACCGA-TT
1 CAACTCGT-ATGAGCTTACCGATTT
* * *
5313918 CACAGCTCGGAGGAGCTTACCGTTTAT
1 CA-A-CTCGTATGAGCTTACCGATT-T
*
5313945 C-ACTTGTATGAGC
1 CAACTCGTATGAGC
5313958 ATACATTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.08
24 28 0.55
25 16 0.31
26 1 0.02
27 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (24 bp):
CAACTCGTATGAGCTTACCGATTT
Found at i:5316492 original size:26 final size:29
Alignment explanation
Indices: 5316470--5316524 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
5316460 ATATTATGTT
5316470 TTAAA-AATAATTATATTAATTATATATG
1 TTAAATAATAATTATATTAATTATATATG
*
5316498 TTAAATAATAATTATA-TATTTATATAT
1 TTAAATAATAATTATATTAATTATATAT
5316525 ATTGAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAAATAATAATTATATTAATTATATATG
Found at i:5335318 original size:91 final size:86
Alignment explanation
Indices: 5335210--5335371 Score: 234
Period size: 91 Copynumber: 1.8 Consensus size: 86
5335200 GCAAAGACAG
* *
5335210 AAATTTTCGTTTATTTTTTACACATGTTCTAGTATATAGGAAATTTTTTCATTTTAGTATATAGG
1 AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAA----AT-ATTTTAGTATATAGG
5335275 TTAGCAATAAACTAATTCAATTGGTA
61 TTAGCAATAAACTAATTCAATTGGTA
** *
5335301 AAATTTTCATTTATTTTTTATGCATGTTTTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
1 AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
5335366 AATAAA
66 AATAAA
5335372 TAGGTTTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
86 26 0.39
87 1 0.02
91 39 0.59
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (86 bp):
AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
AATAAACTAATTCAATTGGTA
Found at i:5342826 original size:25 final size:25
Alignment explanation
Indices: 5342790--5342963 Score: 74
Period size: 25 Copynumber: 7.0 Consensus size: 25
5342780 CCGCAACTCT
*
5342790 TTTG-AGCGTCCCGATATATGGCTC
1 TTTGAAGCTTCCCGATATATGGCTC
* * ***
5342814 TTTGAAGCTTCCCAATAAAAATCTC
1 TTTGAAGCTTCCCGATATATGGCTC
* * *
5342839 TTTCATGAGCTTCCCGAT-TAAAGACTC
1 TTTGA--AGCTTCCCGATAT-ATGGCTC
* *
5342866 TCTGGAGCTTCCCGATAT-TGGCTC
1 TTTGAAGCTTCCCGATATATGGCTC
* *
5342890 GCTTGAACCTTCCCG-TCAT-TGGCTC
1 -TTTGAAGCTTCCCGAT-ATATGGCTC
* *
5342915 GTATG-AGCTTCCCGTTA-ATGGCTC
1 -TTTGAAGCTTCCCGATATATGGCTC
* * * *
5342939 TTTGGAGCTTTCCGTTACATGGCTC
1 TTTGAAGCTTCCCGATATATGGCTC
5342964 ACATGGGCTT
Statistics
Matches: 114, Mismatches: 25, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
23 3 0.03
24 35 0.31
25 58 0.51
26 1 0.01
27 17 0.15
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
TTTGAAGCTTCCCGATATATGGCTC
Found at i:5342936 original size:24 final size:23
Alignment explanation
Indices: 5342843--5342963 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 23
5342833 AATCTCTTTC
* *
5342843 ATGAGCTTCCCGATTAAAGACTCT
1 ATGAGCTTCCCG-TTAATGGCTCT
* * *
5342867 CTGGAGCTTCCCGATATTGGCTCGCT
1 AT-GAGCTTCCCGTTAATGGCT--CT
* * *
5342893 -TGAACCTTCCCGTCATTGGCTCGT
1 ATG-AGCTTCCCGTTAATGGCTC-T
5342917 ATGAGCTTCCCGTTAATGGCTCT
1 ATGAGCTTCCCGTTAATGGCTCT
* *
5342940 TTGGAGCTTTCCGTTACATGGCTC
1 AT-GAGCTTCCCGTTA-ATGGCTC
5342964 ACATGGGCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
23 3 0.04
24 36 0.47
25 35 0.46
26 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (23 bp):
ATGAGCTTCCCGTTAATGGCTCT
Found at i:5345283 original size:28 final size:28
Alignment explanation
Indices: 5345243--5345331 Score: 126
Period size: 28 Copynumber: 3.2 Consensus size: 28
5345233 TATACAGTAT
* *
5345243 CAGT-ACAATGTGGGCCTTAGCCTATTA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
* *
5345270 TAGTAACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
*
5345298 CAGTAACAATGTAGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
5345326 CAGTAA
1 CAGTAA
5345332 TCAGTACAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 3 0.06
28 51 0.94
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (28 bp):
CAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:5345506 original size:25 final size:25
Alignment explanation
Indices: 5345446--5345516 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
5345436 AATATCACAG
*
5345446 CAAAGCTGCCAGTAATAATAACGTA
1 CAAAGCTGCCAGTAATAGTAACGTA
* *
5345471 GCAAAGATGCCAGTAACAGTAACGCT-
1 -CAAAGCTGCCAGTAATAGTAACG-TA
5345497 CAAAGCTGCCAGTAATAGTA
1 CAAAGCTGCCAGTAATAGTA
5345517 TATGTGGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 18 0.46
26 20 0.51
27 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (25 bp):
CAAAGCTGCCAGTAATAGTAACGTA
Found at i:5345740 original size:27 final size:27
Alignment explanation
Indices: 5345705--5346141 Score: 391
Period size: 27 Copynumber: 16.1 Consensus size: 27
5345695 AGGGGTATAA
* *
5345705 CGGTCATTTTACCTTATAG-GGGTATTT
1 CGGTTATTTTACCTT-TCGAGGGTATTT
* *
5345732 CTGTTATTTTACCCTTC-AGGGGTATTT
1 CGGTTATTTTACCTTTCGA-GGGTATTT
*
5345759 CGATTATTTTACCTTTCGAGGGTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
* * *
5345786 TGGTAATTTTACCTTTCAAGGGTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
* * *
5345813 TGGTTATTTTACCATTCGGGGGGTATTT
1 CGGTTATTTTACCTTTC-GAGGGTATTT
*
5345841 CGGTAATTTTACCCTTT-GAGGGTATTT
1 CGGTTATTTTA-CCTTTCGAGGGTATTT
* * * *
5345868 CGATAATTTTACCCTTCGAGGGTTTTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
* * *
5345895 TGGTCATTTTACCCTTCGAGGGTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
** * *
5345922 CAATCATTTTACCATTCGAGGGTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
* *
5345949 CGGTTATTTTACCCTTTAG-GGGCATTT
1 CGGTTATTTTA-CCTTTCGAGGGTATTT
*
5345976 CGGTTATTTTACCATTCGAGGGTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
*
5346003 CGGTTATTTTACCCTTCGAGGGTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
* *
5346030 CGATAATTTTAACC-TTCGAGGGTATTT
1 CGGTTATTTT-ACCTTTCGAGGGTATTT
* * * **
5346057 CGATAATTTTTCCTTTTAAGGGTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
* * * * *
5346084 CGATAATTTTACCCTTCAAGGTTATTT
1 CGGTTATTTTACCTTTCGAGGGTATTT
* * *
5346111 TGATAATTTTACCCTTT-GAGGGTATTT
1 CGGTTATTTTA-CCTTTCGAGGGTATTT
5346138 CGGT
1 CGGT
5346142 CCCATTACGG
Statistics
Matches: 344, Mismatches: 55, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
26 12 0.03
27 298 0.87
28 30 0.09
29 4 0.01
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (27 bp):
CGGTTATTTTACCTTTCGAGGGTATTT
Found at i:5345958 original size:81 final size:81
Alignment explanation
Indices: 5345724--5346142 Score: 455
Period size: 81 Copynumber: 5.2 Consensus size: 81
5345714 TACCTTATAG
* * * * * *
5345724 GGGTATTTCTGTTATTTTACCCTTC-AGGGGTATTTCGATTATTTTACCTTTCGAGGGTATTTTG
1 GGGTATTTCGGTCATTTTACCATTCGA-GGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCG
* * *
5345788 GTAATTTTACCTTTCAA
65 ATAATTTTACCCTTCGA
* * * * *
5345805 GGGTATTTTGGTTATTTTACCATTCGGGGGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCG
1 GGGTATTTCGGTCATTTTACCATTC-GAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCG
5345870 ATAATTTTACCCTTCGA
65 ATAATTTTACCCTTCGA
* * * * * * *
5345887 GGGTTTTTTGGTCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCATTCGAGGGTATTTCGG
1 GGGTATTTCGGTCATTTTACCATTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGA
* *
5345952 TTATTTTACCCTT-TA
66 TAATTTTACCCTTCGA
* * * *
5345967 GGGGCATTTCGGTTATTTTACCATTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTCG
1 -GGGTATTTCGGTCATTTTACCATTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCG
*
5346032 ATAATTTTAACCTTCGA
65 ATAATTTTACCCTTCGA
* * * * ** * * *
5346049 GGGTATTTCGATAATTTTTCCTTTTAAGGGTATTTCGATAATTTTACCCTTCAAGGTTATTTTGA
1 GGGTATTTCGGTCATTTTACCATTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGA
*
5346114 TAATTTTACCCTTTGA
66 TAATTTTACCCTTCGA
5346130 GGGTATTTCGGTC
1 GGGTATTTCGGTC
5346143 CCATTACGGC
Statistics
Matches: 281, Mismatches: 53, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
80 1 0.00
81 211 0.75
82 69 0.25
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (81 bp):
GGGTATTTCGGTCATTTTACCATTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGA
TAATTTTACCCTTCGA
Found at i:5348802 original size:30 final size:30
Alignment explanation
Indices: 5348768--5348836 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
5348758 ACAAAAAAAT
5348768 AAATTACATTTTAGCCCCAGAACTTTTCAA
1 AAATTACATTTTAGCCCCAGAACTTTTCAA
* * *
5348798 AAATTACATTTTAGCCCCTGTATTTTTCAA
1 AAATTACATTTTAGCCCCAGAACTTTTCAA
5348828 AAATTACAT
1 AAATTACAT
5348837 CTTGACCCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (30 bp):
AAATTACATTTTAGCCCCAGAACTTTTCAA
Found at i:5348874 original size:29 final size:29
Alignment explanation
Indices: 5348828--5348897 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
5348818 TATTTTTCAA
*
5348828 AAATTACATCTTGACCCCTAATA-TTT-TGT
1 AAATTACA-CTTGACCCCTAA-ACTTTCTAT
*
5348857 AAATTACACTTAGGCCCCTAAACTTTCTAT
1 AAATTACACTT-GACCCCTAAACTTTCTAT
5348887 AAATTACACTT
1 AAATTACACTT
5348898 TAGCCCTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 4 0.11
29 19 0.53
30 13 0.36
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (29 bp):
AAATTACACTTGACCCCTAAACTTTCTAT
Found at i:5348918 original size:29 final size:30
Alignment explanation
Indices: 5348766--5348918 Score: 95
Period size: 30 Copynumber: 5.2 Consensus size: 30
5348756 ATACAAAAAA
* *
5348766 ATAAATTACATTTTAGCCCC-AGAACTTTT-C
1 ATAAATTACACTTTAGCCCCTA-TA-TTTTCC
* * * *
5348796 AAAAATTACATTTTAGCCCCTGTATTTTTC
1 ATAAATTACACTTTAGCCCCTATATTTTCC
* *
5348826 AAAAATTACATCTTGA-CCCCTAATATTTT--
1 ATAAATTACA-CTTTAGCCCCT-ATATTTTCC
* * * *
5348855 GTAAATTACAC-TTAGGCCCCTAAACTTTCT
1 ATAAATTACACTTTA-GCCCCTATATTTTCC
5348885 ATAAATTACACTTTAG-CCCTATATTTTCC
1 ATAAATTACACTTTAGCCCCTATATTTTCC
*
5348914 CTAAA
1 ATAAA
5348919 ATTGCATTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
27 2 0.02
28 6 0.06
29 31 0.32
30 47 0.48
31 12 0.12
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (30 bp):
ATAAATTACACTTTAGCCCCTATATTTTCC
Found at i:5349513 original size:16 final size:16
Alignment explanation
Indices: 5349448--5349523 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
5349438 GCCGAGAAAA
* *
5349448 GAAATAGAAGAGAA-A
1 GAAAGAGAAGAGAAGG
*
5349463 GAAAG-GAGAGAAAAGG
1 GAAAGAGA-AGAGAAGG
5349479 GAAAGAG-AGA-AAGGG
1 GAAAGAGAAGAGAA-GG
5349494 GAAAGAGAAGAGAAGG
1 GAAAGAGAAGAGAAGG
5349510 GAAAGAGAAGAGAA
1 GAAAGAGAAGAGAA
5349524 AAAGGAAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
14 4 0.08
15 21 0.40
16 24 0.46
17 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.01
Consensus pattern (16 bp):
GAAAGAGAAGAGAAGG
Found at i:5349517 original size:11 final size:11
Alignment explanation
Indices: 5349441--5349524 Score: 52
Period size: 11 Copynumber: 8.0 Consensus size: 11
5349431 TGGGGTTGCC
*
5349441 GAGAAAAGAAA
1 GAGAAGAGAAA
*
5349452 TAGAAGAGAAA
1 GAGAAGAGAAA
*
5349463 GA-AAG-GAGA
1 GAGAAGAGAAA
* *
5349472 GAAAAGGGAAA
1 GAGAAGAGAAA
*
5349483 GAG-AGA-AAG
1 GAGAAGAGAAA
*
5349492 GGGAA-AGAGAA
1 GAGAAGAGA-AA
*
5349503 GAGAAGGGAAA
1 GAGAAGAGAAA
5349514 GAGAAGAGAAA
1 GAGAAGAGAAA
5349525 AAGGAAAAGA
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
9 10 0.19
10 10 0.19
11 32 0.59
12 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.38, T:0.01
Consensus pattern (11 bp):
GAGAAGAGAAA
Found at i:5349531 original size:49 final size:46
Alignment explanation
Indices: 5349448--5349560 Score: 115
Period size: 49 Copynumber: 2.4 Consensus size: 46
5349438 GCCGAGAAAA
* * *
5349448 GAAATAGAAGAGAAAGAAAGGAGAG-AAAAGGGAAAGAGAGAAAGGG
1 GAAAGAGAAGAGAAAGAAAGGAGAGAAAAAGGAAAAGA-AGAAAAGG
*
5349494 GAAAGAGAAGAGAAGGGAAAGAGAAGAGAAAAAGGAAAAGAAGAAAAGG
1 GAAAGAGAAGAGAA-AGAAAG-G-AGAGAAAAAGGAAAAGAAGAAAAGG
5349543 GAGGAAGA-AAGA-AAAGAA
1 GA--AAGAGAAGAGAAAGAA
5349561 TAGAAGGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
46 13 0.23
47 5 0.09
48 4 0.07
49 15 0.27
50 15 0.27
51 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.01
Consensus pattern (46 bp):
GAAAGAGAAGAGAAAGAAAGGAGAGAAAAAGGAAAAGAAGAAAAGG
Found at i:5349533 original size:19 final size:21
Alignment explanation
Indices: 5349496--5349534 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5349486 AGAAAGGGGA
*
5349496 AAGAGAAGAGAAGGGAAAGAG
1 AAGAGAAGAGAAGGAAAAGAG
5349517 AAGAGAA-A-AAGGAAAAGA
1 AAGAGAAGAGAAGGAAAAGA
5349535 AGAAAAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (21 bp):
AAGAGAAGAGAAGGAAAAGAG
Found at i:5349691 original size:10 final size:10
Alignment explanation
Indices: 5349640--5349698 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
5349630 CTTGGGCTCA
5349640 AAAGAAAGAA-
1 AAAGAAA-AAG
*
5349650 AAAGTAAAAG
1 AAAGAAAAAG
* *
5349660 GAAGAAGAAG
1 AAAGAAAAAG
*
5349670 -AAGAAAGGAG
1 AAAGAAA-AAG
5349680 AAAGAAAAAG
1 AAAGAAAAAG
5349690 AAAGAAAAA
1 AAAGAAAAA
5349699 AGAATAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 7 0.18
10 26 0.67
11 6 0.15
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:5349700 original size:17 final size:17
Alignment explanation
Indices: 5349644--5349702 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
5349634 GGCTCAAAAG
5349644 AAAGAAAAAGTAAAAGGAA
1 AAAGAAAAAG--AAAGGAA
* * *
5349663 GAAGAAGAAGAAAGGAG
1 AAAGAAAAAGAAAGGAA
*
5349680 AAAGAAAAAGAAAGAAA
1 AAAGAAAAAGAAAGGAA
5349697 AAAGAA
1 AAAGAA
5349703 TAAAAGCAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 25 0.76
19 8 0.24
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAGAAAGGAA
Found at i:5349893 original size:19 final size:18
Alignment explanation
Indices: 5349864--5349899 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5349854 GCTTTGGTAA
5349864 ATTTTTTTAATCTATTTT
1 ATTTTTTTAATCTATTTT
*
5349882 ATTTTATTTAATGTATTT
1 ATTTT-TTTAATCTATTT
5349900 AAATGGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTTTTAATCTATTTT
Found at i:5350569 original size:19 final size:17
Alignment explanation
Indices: 5350541--5350603 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
5350531 AATTTCCGTG
5350541 TTTCAAAAATTATCATGT
1 TTTCAAAAATT-TCATGT
*
5350559 TTTCAAAAAATTC-TCGT
1 TTTCAAAAATTTCAT-GT
*
5350576 GTTTCACAAATGTTCATGT
1 -TTTCAAAAAT-TTCATGT
5350595 TTTCAAAAA
1 TTTCAAAAA
5350604 AAATTTCGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 26 0.70
19 5 0.14
20 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (17 bp):
TTTCAAAAATTTCATGT
Found at i:5350577 original size:36 final size:36
Alignment explanation
Indices: 5350530--5350619 Score: 121
Period size: 36 Copynumber: 2.4 Consensus size: 36
5350520 TGTCTTGTAG
5350530 AAATTTCCGTGTTTCAAAAAT-TATCATGTTTTC-AAA
1 AAATTT-CGTGTTTCAAAAATGT-TCATGTTTTCAAAA
*
5350566 AAATTCTCGTGTTTCACAAATGTTCATGTTTTCAAAAA
1 AAATT-TCGTGTTTCAAAAATGTTCATGTTTTC-AAAA
5350604 AAATTTCGTGTTTCAA
1 AAATTTCGTGTTTCAA
5350620 TCGGGTCACG
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
36 28 0.58
37 12 0.25
38 8 0.17
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (36 bp):
AAATTTCGTGTTTCAAAAATGTTCATGTTTTCAAAA
Found at i:5351375 original size:35 final size:35
Alignment explanation
Indices: 5351306--5351476 Score: 174
Period size: 35 Copynumber: 4.9 Consensus size: 35
5351296 AACAAAAGTT
*
5351306 TTTTTAAAACACGAGAA-TTTGT--AAACACGAAAA
1 TTTTTAAAACACGA-AATTTTTTAGAAACACGAAAA
*
5351339 -TTTTAGAAACACGAAATTTTTTAGAAAAACGAAAA
1 TTTTTA-AAACACGAAATTTTTTAGAAACACGAAAA
* * **
5351374 TTTTTAAAACACGACATTTTTTTTTGAAACACGGGAA
1 TTTTTAAAACACGA-A-ATTTTTTAGAAACACGAAAA
*
5351411 TTTTTAAAACAGGGAAA--TTTTAGAAACACGAAAA
1 TTTTTAAAACA-CGAAATTTTTTAGAAACACGAAAA
* *
5351445 TTTTTAAAACACGACATTTTTTTGAAACACGA
1 TTTTTAAAACACGAAATTTTTTAGAAACACGA
5351477 TTTAAAAAAC
Statistics
Matches: 113, Mismatches: 15, Indels: 18
0.77 0.10 0.12
Matches are distributed among these distances:
32 7 0.06
33 15 0.13
34 25 0.22
35 31 0.27
36 6 0.05
37 27 0.24
38 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (35 bp):
TTTTTAAAACACGAAATTTTTTAGAAACACGAAAA
Found at i:5351376 original size:19 final size:18
Alignment explanation
Indices: 5351339--5351395 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
5351329 AACACGAAAA
*
5351339 TTTTAGAAACACGAAATT
1 TTTTAGAAAAACGAAATT
*
5351357 TTTTAGAAAAACGAAAAT
1 TTTTAGAAAAACGAAATT
* *
5351375 TTTTA-AAACACGACATT
1 TTTTAGAAAAACGAAATT
5351392 TTTT
1 TTTT
5351396 TTTGAAACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.37
Consensus pattern (18 bp):
TTTTAGAAAAACGAAATT
Found at i:5351429 original size:89 final size:88
Alignment explanation
Indices: 5351304--5351476 Score: 231
Period size: 89 Copynumber: 2.0 Consensus size: 88
5351294 AAAACAAAAG
*
5351304 TTTTTTTAAAACACGAGAATTTGTAAACACGAAAATTTTAGAAACACGAAATTTTTTAGAAAAAC
1 TTTTTTTAAAACACGAGAATTTGTAAACACGAAAATTTTAGAAACACGAAAATTTTTA-AAAAAC
5351369 GA-AAATTTTTAAAACACGACATT
65 GACAAATTTTTAAAACACGACATT
* * * * * *
5351392 TTTTTTTGAAACACGGGAATTTTTAAAACAGGGAAATTTTAGAAACACGAAAATTTTTAAAACAC
1 TTTTTTTAAAACACGAGAATTTGT-AAACACGAAAATTTTAGAAACACGAAAATTTTTAAAAAAC
** *
5351457 GACATTTTTTTGAAACACGA
65 GACAAATTTTTAAAACACGA
5351477 TTTAAAAAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
88 28 0.38
89 45 0.62
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (88 bp):
TTTTTTTAAAACACGAGAATTTGTAAACACGAAAATTTTAGAAACACGAAAATTTTTAAAAAACG
ACAAATTTTTAAAACACGACATT
Found at i:5351564 original size:51 final size:50
Alignment explanation
Indices: 5351509--5351613 Score: 122
Period size: 52 Copynumber: 2.1 Consensus size: 50
5351499 GCTAGAATAT
* *** * *
5351509 TTTGAAACA-CGAATTTTTTTTTAACGCGAGAATTTTTGAAAACATGAAAA
1 TTTGAAACACCGAAGTTTTTGAAAACACGAGAATTTGTG-AAACATGAAAA
*
5351559 CTTTGAAACACCGGAGTTTTTGAAAACACGAGAATTTGTGAAACATGAAAA
1 -TTTGAAACACCGAAGTTTTTGAAAACACGAGAATTTGTGAAACATGAAAA
5351610 TTTG
1 TTTG
5351614 TAAAAACACG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
50 4 0.09
51 20 0.43
52 22 0.48
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (50 bp):
TTTGAAACACCGAAGTTTTTGAAAACACGAGAATTTGTGAAACATGAAAA
Found at i:5351658 original size:93 final size:92
Alignment explanation
Indices: 5351541--5351716 Score: 228
Period size: 93 Copynumber: 1.9 Consensus size: 92
5351531 AACGCGAGAA
* * * * *
5351541 TTTTTGAAAACATGAAAACTTTGAAACACCGGAGTTTTTGAAAACACG-AGAATTTGTGAAACAT
1 TTTTTGAAAACACGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAG-ATTTGTAAAACAC
5351605 GAAAATTTGTAAAAACACGTAATAATTT
65 GAAAATTTGTAAAAACACGTAATAATTT
* * * *
5351633 TTTTTTAAAACACGAAAATTTTTGAAACGCCAGAATTTTTGAAAACACGAAGATTTTTAAAACAC
1 TTTTTGAAAACACGAAAA-CTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTGTAAAACAC
* *
5351698 GAAAATTTTTGAAAACACG
65 GAAAATTTGTAAAAACACG
5351717 AAAACACAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
92 16 0.23
93 53 0.75
94 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (92 bp):
TTTTTGAAAACACGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTGTAAAACACG
AAAATTTGTAAAAACACGTAATAATTT
Found at i:5351678 original size:35 final size:35
Alignment explanation
Indices: 5351633--5351796 Score: 125
Period size: 35 Copynumber: 4.5 Consensus size: 35
5351623 GTAATAATTT
* * * *
5351633 TTTTTTAAAACACGAAAATTTTTGAAACGCCAGAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACCAAAA
* *
5351668 TTTTTGAAAACACGAAGATTTTTAAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACCAAAA
** * **
5351703 TTTTTGAAAACACGAAAACACAAAATTTTTCGAACACGGAATT
1 TTTTTGAAAACACG-------AAAATTTTTAAAACAC-CAAAA
* *
5351746 TTTTTGAAAACACGATAA--TTTAAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACCAAAA
5351779 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
5351797 CACAAAATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
33 20 0.19
34 8 0.08
35 43 0.41
36 3 0.03
42 13 0.12
43 17 0.16
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACCAAAA
Found at i:5351718 original size:18 final size:18
Alignment explanation
Indices: 5351305--5351796 Score: 179
Period size: 17 Copynumber: 28.0 Consensus size: 18
5351295 AAACAAAAGT
* *
5351305 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
5351323 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
5351339 TTTTAG-AAACACGAAAT
1 TTTTTGAAAACACGAAAA
5351356 TTTTTAGAAAA-ACGAAAA
1 TTTTT-GAAAACACGAAAA
**
5351374 TTTTT-AAAACACGACATTTT
1 TTTTTGAAAACACGA-A--AA
**
5351394 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
5351411 TTTTT-AAAACAGGGAAA
1 TTTTTGAAAACACGAAAA
*
5351428 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
5351445 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
5351463 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
*
5351477 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
* * *
5351491 --ATTGAAATGCTA-GAATA
1 TTTTTGAAA-AC-ACGAAAA
*
5351508 -TTTTG-AAACACG-AAT
1 TTTTTGAAAACACGAAAA
*** * *
5351523 TTTTTTTTAACGCGAGAA
1 TTTTTGAAAACACGAAAA
*
5351541 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
5351559 -CTTTG-AAACACCG-GAG
1 TTTTTGAAAACA-CGAAAA
*
5351575 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
5351593 TTTGTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
* *
5351610 TTTGTAAAAACACGTAATAA
1 TTTTTGAAAACACG-AA-AA
*
5351630 TTTTTTTTTAAAACACGAAAA
1 ---TTTTTGAAAACACGAAAA
* * *
5351651 TTTTTG-AAACGCCAGAA
1 TTTTTGAAAACACGAAAA
*
5351668 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
5351686 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
5351703 TTTTTGAAAACACGAAAACACAAAA
1 TTTTTGAAAACACG-------AAAA
**
5351728 TTTTTCG--AACACGGAATT
1 TTTTT-GAAAACAC-GAAAA
*
5351746 TTTTTGAAAACACGATAA
1 TTTTTGAAAACACGAAAA
5351764 --TTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
5351779 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
5351797 CACAAAATTT
Statistics
Matches: 351, Mismatches: 70, Indels: 106
0.67 0.13 0.20
Matches are distributed among these distances:
12 8 0.02
14 3 0.01
15 16 0.05
16 32 0.09
17 127 0.36
18 109 0.31
19 10 0.03
20 14 0.04
21 2 0.01
22 2 0.01
23 12 0.03
24 5 0.01
25 10 0.03
26 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:5351747 original size:76 final size:75
Alignment explanation
Indices: 5351639--5351840 Score: 295
Period size: 76 Copynumber: 2.6 Consensus size: 75
5351629 ATTTTTTTTT
5351639 AAAACACGAAAATTTTT-GAA-ACGCCAGAA-TTTTTGAAAACACGA-AGATTTTTAAAACACGA
1 AAAACAC-AAAATTTTTCGAACACG---GAATTTTTTGAAAACACGATA-A--TTTAAAACACGA
5351700 AAATTTTTGAAAACACG
59 AAATTTTTGAAAACACG
5351717 AAAACACAAAATTTTTCGAACACGGAATTTTTTTGAAAACACGATAATTTAAAACACGAAAATTT
1 AAAACACAAAATTTTTCGAACACGGAA-TTTTTTGAAAACACGATAATTTAAAACACGAAAATTT
5351782 TTGAAAACACG
65 TTGAAAACACG
5351793 AAAACACAAAATTTTTCGAACACGGAATTTTTTAGAAAACACGATAAT
1 AAAACACAAAATTTTTCGAACACGGAATTTTTT-GAAAACACGATAAT
5351841 ATCAAAAAAT
Statistics
Matches: 118, Mismatches: 0, Indels: 14
0.89 0.00 0.11
Matches are distributed among these distances:
75 6 0.05
76 73 0.62
77 9 0.08
78 26 0.22
79 4 0.03
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (75 bp):
AAAACACAAAATTTTTCGAACACGGAATTTTTTGAAAACACGATAATTTAAAACACGAAAATTTT
TGAAAACACG
Found at i:5351772 original size:15 final size:15
Alignment explanation
Indices: 5351752--5351796 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
5351742 AATTTTTTTG
*
5351752 AAAACACGATAATTT
1 AAAACACGAAAATTT
5351767 AAAACACGAAAATTTTT
1 AAAACACGAAAA--TTT
5351784 GAAAACACGAAAA
1 -AAAACACGAAAA
5351797 CACAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.42
17 3 0.12
18 12 0.46
ACGTcount: A:0.58, C:0.13, G:0.09, T:0.20
Consensus pattern (15 bp):
AAAACACGAAAATTT
Found at i:5351900 original size:18 final size:17
Alignment explanation
Indices: 5351879--5351928 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 17
5351869 TATTTATTTA
5351879 TTTTTTGAAACACGAGAT
1 TTTTTTGAAACACGA-AT
*
5351897 TTTTTCGAAAACACGAAT
1 TTTTTTG-AAACACGAAT
5351915 TTTTTTGAAACACG
1 TTTTTTGAAACACG
5351929 GGAATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.24
18 14 0.48
19 8 0.28
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTTTTGAAACACGAAT
Found at i:5351908 original size:19 final size:16
Alignment explanation
Indices: 5351878--5351928 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 16
5351868 TTATTTATTT
5351878 ATTTTTTGAAACACGA
1 ATTTTTTGAAACACGA
5351894 GATTTTTTCGAAAACACGA
1 -ATTTTTT-G-AAACACGA
5351913 ATTTTTTTGAAACACG
1 A-TTTTTTGAAACACG
5351929 GGAATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 14 0.45
18 3 0.10
19 14 0.45
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (16 bp):
ATTTTTTGAAACACGA
Found at i:5351924 original size:36 final size:35
Alignment explanation
Indices: 5351879--5351954 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
5351869 TATTTATTTA
* **
5351879 TTTTTTGAAACACGAGATTTTTTCGAAAACACGAAT
1 TTTTTTGAAACACGAGAATTTTTAAAAAACACG-AT
* *
5351915 TTTTTTGAAACACGGGAATTTTTAAAAAAGACGAT
1 TTTTTTGAAACACGAGAATTTTTAAAAAACACGAT
5351950 TTTTT
1 TTTTT
5351955 AAGAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 7 0.20
36 28 0.80
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTTTTGAAACACGAGAATTTTTAAAAAACACGAT
Found at i:5351933 original size:19 final size:18
Alignment explanation
Indices: 5351879--5351937 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
5351869 TATTTATTTA
5351879 TTTTTTGAAACAC-GAGAT
1 TTTTTTGAAACACGGA-AT
*
5351897 TTTTTCGAAAACAC-GAAT
1 TTTTTTG-AAACACGGAAT
5351915 TTTTTTGAAACACGGGAAT
1 TTTTTTGAAACAC-GGAAT
5351934 TTTT
1 TTTT
5351938 AAAAAAGACG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 6 0.17
18 14 0.39
19 16 0.44
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (18 bp):
TTTTTTGAAACACGGAAT
Found at i:5352907 original size:5 final size:5
Alignment explanation
Indices: 5352897--5352948 Score: 65
Period size: 5 Copynumber: 11.0 Consensus size: 5
5352887 AGTCTCGGCG
* *
5352897 TTCTC TTCTC TTCTT TTCTC TTCCC TT-T- TTCTC TTC-C TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC
5352944 TTCTC
1 TTCTC
5352949 CCTTTGACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 5 0.12
5 33 0.82
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCTC
Found at i:5352996 original size:36 final size:35
Alignment explanation
Indices: 5352920--5352999 Score: 88
Period size: 36 Copynumber: 2.3 Consensus size: 35
5352910 TTTTCTCTTC
* **
5352920 CCTTTTTCTCTTCCTTCTCTTCTCTTCTCCCTTTG
1 CCTTTCTCTCTTCCTTCTCTTCTCCCCTCCCTTTG
* * * *
5352955 ACTTTCTCTCTTTTCTTCTCTTCTCCCCTCTCTTTT
1 CCTTTCTCTC-TTCCTTCTCTTCTCCCCTCCCTTTG
5352991 CCTTTCTCT
1 CCTTTCTCT
5353000 TTCGCAAGCC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
35 8 0.22
36 28 0.78
ACGTcount: A:0.01, C:0.40, G:0.01, T:0.57
Consensus pattern (35 bp):
CCTTTCTCTCTTCCTTCTCTTCTCCCCTCCCTTTG
Found at i:5353550 original size:29 final size:30
Alignment explanation
Indices: 5353509--5353692 Score: 143
Period size: 29 Copynumber: 6.3 Consensus size: 30
5353499 GGCAAAAACA
*
5353509 TAATTT-TAGGAAAATAT-GGGGCTAAAATG
1 TAATTTATA-GAAAATTTAGGGGCTAAAATG
* **
5353538 TAATTTATAGAAAGTTTAGGGGCCCAAATG
1 TAATTTATAGAAAATTTAGGGGCTAAAATG
*
5353568 CAA-TT-TAGAAAAGTTTAGGGG-TAGAAATG
1 TAATTTATAGAAAA-TTTAGGGGCTA-AAATG
* * *
5353597 TAATTT-TGAGAAAGTTTAGGGGGTGAAATG
1 TAATTTAT-AGAAAATTTAGGGGCTAAAATG
* * *
5353627 TAATTTCA-A-AAAGTTTAGGGGTTGAAATG
1 TAATTT-ATAGAAAATTTAGGGGCTAAAATG
* *
5353656 TAATTTAGA-AAAATTTAGGGGCCAAAATG
1 TAATTTATAGAAAATTTAGGGGCTAAAATG
5353685 TAATTTAT
1 TAATTTAT
5353693 GTTTTTTTTA
Statistics
Matches: 128, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
28 7 0.05
29 78 0.61
30 37 0.29
31 6 0.05
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (30 bp):
TAATTTATAGAAAATTTAGGGGCTAAAATG
Found at i:5353567 original size:30 final size:29
Alignment explanation
Indices: 5353533--5353692 Score: 162
Period size: 29 Copynumber: 5.4 Consensus size: 29
5353523 TATGGGGCTA
*
5353533 AAATGTAATTTATAGAAAGTTTAGGGGCCC
1 AAATGTAATTTATA-AAAGTTTAGGGGCCG
* * **
5353563 AAATGCAATTTAGAAAAGTTTAGGGGTAG
1 AAATGTAATTTATAAAAGTTTAGGGGCCG
**
5353592 AAATGTAATTT-TGAGAAAGTTTAGGGGGTG
1 AAATGTAATTTAT-A-AAAGTTTAGGGGCCG
**
5353622 AAATGTAATTTCA-AAAAGTTTAGGGGTTG
1 AAATGTAATTT-ATAAAAGTTTAGGGGCCG
* * *
5353651 AAATGTAATTTAGAAAAATTTAGGGGCCA
1 AAATGTAATTTATAAAAGTTTAGGGGCCG
5353680 AAATGTAATTTAT
1 AAATGTAATTTAT
5353693 GTTTTTTTTA
Statistics
Matches: 110, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.01
29 72 0.65
30 37 0.34
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (29 bp):
AAATGTAATTTATAAAAGTTTAGGGGCCG
Found at i:5353596 original size:59 final size:58
Alignment explanation
Indices: 5353533--5353691 Score: 205
Period size: 59 Copynumber: 2.7 Consensus size: 58
5353523 TATGGGGCTA
* *
5353533 AAATGTAATTTATAGAAAGTTTAGGGGCCCAAATGCAATTTAGAAAAGTTTAGGGGTAG
1 AAATGTAATTTATAGAAAGTTTAGGGGCCAAAATGTAATTTA-AAAAGTTTAGGGGTAG
*** *
5353592 AAATGTAATTT-TGAGAAAGTTTAGGGGGTGAAATGTAATTTCAAAAAGTTTAGGGGTTG
1 AAATGTAATTTAT-AGAAAGTTTAGGGGCCAAAATGTAATTT-AAAAAGTTTAGGGGTAG
* *
5353651 AAATGTAATTTAGA-AAAATTTAGGGGCCAAAATGTAATTTA
1 AAATGTAATTTATAGAAAGTTTAGGGGCCAAAATGTAATTTA
5353692 TGTTTTTTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
57 1 0.01
58 23 0.26
59 62 0.71
60 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (58 bp):
AAATGTAATTTATAGAAAGTTTAGGGGCCAAAATGTAATTTAAAAAGTTTAGGGGTAG
Found at i:5354139 original size:78 final size:76
Alignment explanation
Indices: 5354054--5354196 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 76
5354044 TGAAAAATAG
* * * *
5354054 AAATTGAAGAATACCTCGGCATATGAC-CTAAGGCTCAACTCACCTCTTGTAATATGAGTTGATT
1 AAATTGAAAAATACCTC-G-ACATGACTC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
5354118 TTTGTGAAAATCAA
63 TTTGTGAAAATCAA
* *
5354132 AAATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAAATACCTCGACATGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5354197 TTCCTTTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
76 40 0.69
77 2 0.03
78 16 0.28
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (76 bp):
AAATTGAAAAATACCTCGACATGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GTGAAAATCAA
Found at i:5354228 original size:88 final size:88
Alignment explanation
Indices: 5354122--5354285 Score: 276
Period size: 88 Copynumber: 1.9 Consensus size: 88
5354112 TTGATTTTTG
* *
5354122 TGAAAATCAAAAATTGAAAAATACCTCGACG-TGACTCGAGGCTCAACTCACCTCTCGCAATATG
1 TGAAAAACAAAAATTGAAAAATACCTC-ACGATGACCCGAGGCTCAACTCACCTCTCGCAATATG
5354186 AGTTGATTTTTTTCCTTTTTCTTT
65 AGTTGATTTTTTTCCTTTTTCTTT
* *
5354210 TGAAAAACAAAAATTGAAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCATTATGA
1 TGAAAAACAAAAATTGAAAAATACCTCACGATGACCCGAGGCTCAACTCACCTCTCGCAATATGA
5354275 GTTGATTTTTT
66 GTTGATTTTTT
5354286 GAAAAACAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 2 0.03
88 69 0.97
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (88 bp):
TGAAAAACAAAAATTGAAAAATACCTCACGATGACCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTCCTTTTTCTTT
Found at i:5354590 original size:79 final size:79
Alignment explanation
Indices: 5354226--5355327 Score: 1645
Period size: 79 Copynumber: 13.8 Consensus size: 79
5354216 ACAAAAATTG
* *
5354226 AAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AA
1 AAAAAAACCTCAGCG-TGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAA
*
5354289 AAA-CAAAAATTTTAAA
64 AAAGCAGAAA-TTTAAA
* * * *
5354305 AGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCGA-TATGAGTTGATTTTTTTG
1 AAAAAAACCTCAGCGT--GACCCGAGGCTCAACTCACCTCT-G-TATTATGAGTTGA-TTTTTTG
* **
5354369 AAAAATAG-AAAAACATAAA
61 AAAAA-AGCAGAAATTTAAA
* * * *
5354388 TTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTTTCGCATTATGAGTTGATTTTTTGAA
1 --AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAA
*
5354453 AAAA-CAGAAATTAAATTA
63 AAAAGCAGAAATTTAA--A
5354471 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAA
1 AAAAAA-ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAA
5354536 AAGCAGAAATTTAAA
65 AAGCAGAAATTTAAA
*
5354551 AAAAAAACCTCTGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
5354616 AGCAGAAATTTAAA
66 AGCAGAAATTTAAA
*
5354630 AAAAAAACCTCTGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
5354695 AGCAGAAATTTAAA
66 AGCAGAAATTTAAA
*
5354709 AAAAAAACCTCTGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
5354774 AGCAGAAATTTAAA
66 AGCAGAAATTTAAA
*
5354788 AAAAAAACCTCTGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
5354853 AGCAGAAATTTAAA
66 AGCAGAAATTTAAA
*
5354867 AAAAAAACCTCTGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
5354932 AGCAGAAATTTAAA
66 AGCAGAAATTTAAA
*
5354946 AAAAAAACCTCTGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
*
5355011 GGCAGAAATTT---
66 AGCAGAAATTTAAA
* * * *
5355022 AAAAATATCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTAATTTTTCGAAAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
*
5355087 A-CAGAAATTAAATTA
66 AGCAGAAATTTAA--A
5355102 AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAA
1 AAAAAA-ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAA
5355166 AAGCAGAAA-TTAAA
65 AAGCAGAAATTTAAA
*
5355180 AAATAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAA
1 AAA-AAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAA
5355245 AAAGCAGAAA-TTAAA
64 AAAGCAGAAATTTAAA
* *
5355260 AAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTTTTTGAAA
1 AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTTTGAAA
5355325 AAA
64 AAA
5355328 AAAAGAATTT
Statistics
Matches: 960, Mismatches: 35, Indels: 55
0.91 0.03 0.05
Matches are distributed among these distances:
75 8 0.01
76 60 0.06
78 51 0.05
79 533 0.56
80 54 0.06
81 129 0.13
82 63 0.07
83 42 0.04
84 6 0.01
85 14 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (79 bp):
AAAAAAACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
AGCAGAAATTTAAA
Found at i:5356214 original size:7 final size:7
Alignment explanation
Indices: 5356198--5356260 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
5356188 TTCATCTTGA
*
5356198 TTTTTCT
1 TTTTTGT
5356205 TTTTCT-T
1 TTTT-TGT
5356212 TTTTTGT
1 TTTTTGT
5356219 TTTTTGT
1 TTTTTGT
5356226 TTTTTGT
1 TTTTTGT
*
5356233 TTTTTTT
1 TTTTTGT
*
5356240 TGTTATTTT
1 T-TT-TTGT
5356249 TTTTTGT
1 TTTTTGT
5356256 TTTTT
1 TTTTT
5356261 TGTCTACTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
6 1 0.02
7 39 0.78
8 5 0.10
9 5 0.10
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.87
Consensus pattern (7 bp):
TTTTTGT
Found at i:5356222 original size:21 final size:20
Alignment explanation
Indices: 5356198--5356261 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 20
5356188 TTCATCTTGA
*
5356198 TTTTTCTTTTTCTTTTTTTG
1 TTTTTTTTTTTCTTTTTTTG
* *
5356218 TTTTTTGTTTT-TTGTTTT-
1 TTTTTTTTTTTCTTTTTTTG
* *
5356236 TTTTTGTTATT-TTTTTTTG
1 TTTTTTTTTTTCTTTTTTTG
5356255 TTTTTTT
1 TTTTTTT
5356262 GTCTACTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.40
19 12 0.34
20 9 0.26
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTTCTTTTTTTG
Found at i:5356242 original size:24 final size:23
Alignment explanation
Indices: 5356197--5356261 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
5356187 TTTCATCTTG
*
5356197 ATTTTTCTTTT-TCTTTTTTTGTT
1 ATTTTT-TTTTGTTTTTTTTTGTT
*
5356220 TTTTGTTTTTTGTTTTTTTTTGTT
1 ATTT-TTTTTTGTTTTTTTTTGTT
5356244 ATTTTTTTTTGTTTTTTT
1 ATTTTTTTTTGTTTTTTT
5356262 GTCTACTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.86
Consensus pattern (23 bp):
ATTTTTTTTTGTTTTTTTTTGTT
Found at i:5356261 original size:13 final size:13
Alignment explanation
Indices: 5356198--5356261 Score: 71
Period size: 13 Copynumber: 5.0 Consensus size: 13
5356188 TTCATCTTGA
*
5356198 TTTTTCTTTTTCTT
1 TTTTTGTTTTT-TT
5356212 TTTTTGTTTTTTGT
1 TTTTTGTTTTTT-T
5356226 TTTTTG---TTTT
1 TTTTTGTTTTTTT
*
5356236 TTTTTGTTATTTT
1 TTTTTGTTTTTTT
5356249 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
5356262 GTCTACTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
10 7 0.16
11 3 0.07
13 17 0.39
14 17 0.39
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:5356262 original size:21 final size:21
Alignment explanation
Indices: 5356199--5356274 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
5356189 TCATCTTGAT
* *
5356199 TTTTCTTTTTCTTTTTTTGTTT
1 TTTT-TTTTTGTTTTTTTGTTA
5356221 TTTGTTTTTTGTTTTTTTTTGTTA
1 TTT-TTTTTTG--TTTTTTTGTTA
5356245 TTTTTTTTTGTTTTTTTGTCTA
1 TTTTTTTTTGTTTTTTTGT-TA
*
5356267 CTTTTTTT
1 TTTTTTTT
5356275 CAGGCATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 9 0.19
22 17 0.36
23 8 0.17
24 13 0.28
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTGTTTTTTTGTTA
Found at i:5356274 original size:1 final size:1
Alignment explanation
Indices: 5356198--5356261 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
5356188 TTCATCTTGA
* * * * * * * *
5356198 TTTTTCTTTTTCTTTTTTTGTTTTTTGTTTTTTGTTTTTTTTTGTTATTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5356262 GTCTACTTTT
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:5359807 original size:10 final size:10
Alignment explanation
Indices: 5359792--5359820 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5359782 ATCAACACAT
5359792 GATGATATGA
1 GATGATATGA
5359802 GATGATATGA
1 GATGATATGA
5359812 GAT-ATATGA
1 GATGATATGA
5359821 TGGAAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (10 bp):
GATGATATGA
Found at i:5367345 original size:17 final size:17
Alignment explanation
Indices: 5367325--5367683 Score: 102
Period size: 17 Copynumber: 20.8 Consensus size: 17
5367315 AACGAAAGTT
5367325 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
*
5367342 TTTTTGAAAACATGAGAA
1 TTTTT-AAAACACGAGAA
*
5367360 TTTGT-AAACACGA-AA
1 TTTTTAAAACACGAGAA
* *
5367375 ATTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
* *
5367393 TTTTTAGAAAAAACGAAAA
1 TTTTT--AAAACACGAGAA
* *
5367412 TTTTTAAAACACGACATT
1 TTTTTAAAACACGAGA-A
*
5367430 TTTTTGAAACAC--G-A
1 TTTTTAAAACACGAGAA
*
5367444 --TTTAAAAAAC-A-AA
1 TTTTTAAAACACGAGAA
** * **
5367457 -AATTGAAATGCGAGAA
1 TTTTTAAAACACGAGAA
* * *
5367473 TATTTTGAAACATGA-AT
1 T-TTTTAAAACACGAGAA
** *
5367490 TTTTTTTAACGCGAGAA
1 TTTTTAAAACACGAGAA
*
5367507 TTTTTGAAAACATGCA-AA
1 TTTTT-AAAACACG-AGAA
* * *
5367525 -CTTTGAAACACCG-GAG
1 TTTTTAAAACA-CGAGAA
5367541 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAGAA
* * *
5367559 TTTGTGAAACACGAAAA
1 TTTTTAAAACACGAGAA
* *
5367576 TTTGTGAAAACACGTAATAA
1 TTT-TTAAAACACG--AGAA
* *
5367596 TTTTTTTTTAAAACATGAAAA
1 ----TTTTTAAAACACGAGAA
* *
5367617 TTTTTGAAACGTC-AGAA
1 TTTTTAAAAC-ACGAGAA
5367634 TTTTTGAAAACACGA-AGA
1 TTTTT-AAAACACGAGA-A
*
5367652 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAGAA
5367669 TTTTTAAAAACACGA
1 TTTTT-AAAACACGA
5367684 AAACACAAAA
Statistics
Matches: 250, Mismatches: 57, Indels: 69
0.66 0.15 0.18
Matches are distributed among these distances:
12 8 0.03
13 1 0.00
14 6 0.02
15 6 0.02
16 24 0.10
17 86 0.34
18 85 0.34
19 16 0.06
20 4 0.02
21 3 0.01
23 8 0.03
24 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:5367345 original size:18 final size:17
Alignment explanation
Indices: 5367307--5367443 Score: 86
Period size: 18 Copynumber: 7.9 Consensus size: 17
5367297 GCATTATTTC
5367307 TTTTTT-AAA-ACGAAA
1 TTTTTTAAAACACGAAA
5367322 GTTTTTTTAAAACACGAGAA
1 --TTTTTTAAAACACGA-AA
* *
5367342 TTTTTGAAAACATGAGAA
1 TTTTTTAAAACACGA-AA
*
5367360 -TTTGT-AAACACGAAA
1 TTTTTTAAAACACGAAA
*
5367375 -ATTTTAGAAACACGAAAA
1 TTTTTTA-AAACACG-AAA
* *
5367393 TTTTTAGAAAAAACGAAA
1 TTTTT-TAAAACACGAAA
* *
5367411 ATTTTTAAAACACGACAT
1 TTTTTTAAAACACGA-AA
*
5367429 TTTTTTGAAACACGA
1 TTTTTTAAAACACGA
5367444 TTTAAAAAAC
Statistics
Matches: 95, Mismatches: 16, Indels: 17
0.74 0.12 0.13
Matches are distributed among these distances:
15 5 0.05
16 7 0.07
17 24 0.25
18 43 0.45
19 13 0.14
20 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTTTTAAAACACGAAA
Found at i:5367626 original size:93 final size:92
Alignment explanation
Indices: 5367507--5367682 Score: 228
Period size: 93 Copynumber: 1.9 Consensus size: 92
5367497 AACGCGAGAA
* * * *
5367507 TTTTTGAAAACATGCAAACTTTGAAACACCGGAGTTTTTGAAAACACG-AGAATTTGTGAAACAC
1 TTTTTGAAAACATGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAG-ATTTGTAAAACAC
*
5367571 GAAAATTTGTGAAAACACGTAATAATTT
65 GAAAATTTGTAAAAACACGTAATAATTT
* * ** *
5367599 TTTTTTAAAACATGAAAATTTTTGAAACGTCAGAATTTTTGAAAACACGAAGATTTTTAAAACAC
1 TTTTTGAAAACATGAAAA-CTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTGTAAAACAC
*
5367664 GAAAATTTTTAAAAACACG
65 GAAAATTTGTAAAAACACG
5367683 AAAACACAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
92 16 0.23
93 53 0.75
94 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (92 bp):
TTTTTGAAAACATGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTGTAAAACACG
AAAATTTGTAAAAACACGTAATAATTT
Found at i:5367671 original size:35 final size:35
Alignment explanation
Indices: 5367307--5367686 Score: 136
Period size: 35 Copynumber: 11.0 Consensus size: 35
5367297 GCATTATTTC
* * * *
5367307 TTTTTTAAA-ACGAAAGTTTTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAA-ATTTTTGAAAACACGAAAA
* * *
5367342 TTTTTGAAAACATGAGAA--TTTGTAAACACGAAAA
1 TTTTT-AAAACACGAAAATTTTTGAAAACACGAAAA
*
5367376 -TTTTAGAAACACGAAAATTTTTAGAAAAAACGAAAA
1 TTTTTA-AAACACGAAAATTTTT-GAAAACACGAAAA
**
5367412 TTTTTAAAACACGACATTTTTTTG-AAACACG---A
1 TTTTTAAAACACGA-AAATTTTTGAAAACACGAAAA
* * ** *
5367444 --TTTAAAAAAC-AAAA--ATTG-AAATGCGAGAA
1 TTTTTAAAACACGAAAATTTTTGAAAACACGAAAA
* * *** * *
5367473 TATTTTGAAACATG--AATTTTTTTTAACGCGAGAA
1 T-TTTTAAAACACGAAAATTTTTGAAAACACGAAAA
* * * * *
5367507 TTTTTGAAAACATGCAAA-CTTTG-AAACACCG-GAG
1 TTTTT-AAAACACGAAAATTTTTGAAAACA-CGAAAA
* *
5367541 TTTTTGAAAACACGAGAATTTGTG-AAACACGAAAA
1 TTTTT-AAAACACGAAAATTTTTGAAAACACGAAAA
* * *
5367576 TTTGTGAAAACACGTAATAATTTTTTTTTAAAACATGAAAA
1 TTT-TTAAAACACG-AA-AA---TTTTTGAAAACACGAAAA
* * * *
5367617 TTTTTGAAACGTC-AGAATTTTTGAAAACACGAAGA
1 TTTTTAAAAC-ACGAAAATTTTTGAAAACACGAAAA
*
5367652 TTTTTAAAACACGAAAATTTTTAAAAACACGAAAA
1 TTTTTAAAACACGAAAATTTTTGAAAACACGAAAA
5367687 CACAAAATTT
Statistics
Matches: 255, Mismatches: 57, Indels: 66
0.67 0.15 0.17
Matches are distributed among these distances:
26 8 0.03
28 1 0.00
29 2 0.01
30 9 0.04
31 2 0.01
32 9 0.04
33 19 0.07
34 53 0.21
35 82 0.32
36 27 0.11
37 17 0.07
38 2 0.01
39 1 0.00
40 9 0.04
41 14 0.05
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (35 bp):
TTTTTAAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:5367787 original size:18 final size:19
Alignment explanation
Indices: 5367764--5367799 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5367754 TTTTTTATTT
*
5367764 ATTTTTTTG-AAACACGAG
1 ATTTTTTCGAAAACACGAG
5367782 ATTTTTTCGAAAACACGA
1 ATTTTTTCGAAAACACGA
5367800 AAACACGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
ATTTTTTCGAAAACACGAG
Found at i:5367822 original size:17 final size:18
Alignment explanation
Indices: 5367798--5367849 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
5367788 TCGAAAACAC
5367798 GAAAACACGATTTTTTTT
1 GAAAACACGATTTTTTTT
* *
5367816 GAAACACAGGA--ATTTTT
1 GAAA-ACACGATTTTTTTT
5367833 GAAAACACGATTTTTTT
1 GAAAACACGATTTTTTT
5367850 AAAGAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 8 0.30
19 5 0.19
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (18 bp):
GAAAACACGATTTTTTTT
Found at i:5367831 original size:18 final size:16
Alignment explanation
Indices: 5367798--5367848 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
5367788 TCGAAAACAC
5367798 GAAAACACGATTTTTTTT
1 GAAAACACGA--TTTTTT
* *
5367816 GAAACACAGGAATTTTT
1 GAAA-ACACGATTTTTT
5367833 GAAAACACGATTTTTT
1 GAAAACACGATTTTTT
5367849 TAAAGAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 10 0.36
17 9 0.32
18 4 0.14
19 5 0.18
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (16 bp):
GAAAACACGATTTTTT
Found at i:5367906 original size:60 final size:61
Alignment explanation
Indices: 5367842--5367969 Score: 197
Period size: 60 Copynumber: 2.1 Consensus size: 61
5367832 TGAAAACACG
*
5367842 ATTTTTTTAA-AGAAAGAAACACGAATGTATTTTTTTCGAAACACGGGAAATTTTATTATT
1 ATTTTTTTAATAGAAAGAAACACAAATGTATTTTTTTCGAAACACGGGAAATTTTATTATT
** *
5367902 A-TTTTGGAATAGAAAGAAACACAAATGTATTTTTTTCGAAACAGGGGAAATTTTATTATT
1 ATTTTTTTAATAGAAAGAAACACAAATGTATTTTTTTCGAAACACGGGAAATTTTATTATT
*
5367962 ATTATTTT
1 ATTTTTTT
5367970 GAAACACGAG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 6 0.10
60 50 0.85
61 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (61 bp):
ATTTTTTTAATAGAAAGAAACACAAATGTATTTTTTTCGAAACACGGGAAATTTTATTATT
Found at i:5368413 original size:18 final size:17
Alignment explanation
Indices: 5368386--5368420 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5368376 AACACCATTT
5368386 AAATACATTAAATAAAAA
1 AAATACATTAAA-AAAAA
*
5368404 AAATAGATTAAAAAAAA
1 AAATACATTAAAAAAAA
5368421 TTACCAAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATACATTAAAAAAAA
Found at i:5368704 original size:11 final size:10
Alignment explanation
Indices: 5368697--5368731 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
5368687 TTTTTTTTAT
5368697 TTTCTTTTTC
1 TTTCTTTTTC
5368707 TTTCTTTTTC
1 TTTCTTTTTC
*
5368717 TCTCTTTTTC
1 TTTCTTTTTC
5368727 TTTCT
1 TTTCT
5368732 CCCTTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:5368742 original size:20 final size:19
Alignment explanation
Indices: 5368698--5368742 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5368688 TTTTTTTATT
**
5368698 TTCTTTTTCTTTCTTTTTC
1 TTCTTTTTCTTTCTCCTTC
5368717 TCTCTTTTTCTTTCTCCCTTC
1 T-TCTTTTTCTTTCT-CCTTC
5368738 TTCTT
1 TTCTT
5368743 CTTCCCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCTTTTTCTTTCTCCTTC
Found at i:5368863 original size:5 final size:5
Alignment explanation
Indices: 5368853--5368904 Score: 65
Period size: 5 Copynumber: 11.0 Consensus size: 5
5368843 AGTCTCGGCG
* *
5368853 TTCTC TTCTC TTCTT TTCTC TTCCC TT-T- TTCTC TTC-C TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC
5368900 TTCTC
1 TTCTC
5368905 CCTTTGGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 5 0.12
5 33 0.82
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCTC
Found at i:5369502 original size:29 final size:30
Alignment explanation
Indices: 5369449--5369644 Score: 149
Period size: 29 Copynumber: 6.7 Consensus size: 30
5369439 CAAAGTTTTG
* * *
5369449 GGGGCAAAAACGTAATTT-TAGGAAAATAT-
1 GGGGCTAAAATGTAATTTATA-GAAAATTTA
*
5369478 GGGGCTAAAATGTAATTTATAGAAAGTTTA
1 GGGGCTAAAATGTAATTTATAGAAAATTTA
** *
5369508 GGGGCCCAAATGCAA-TT-TAGAAAAGTTTA
1 GGGGCTAAAATGTAATTTATAGAAAA-TTTA
*
5369537 GGGG-TAGAAATGTAATTT-TGAGAAAGTTTA
1 GGGGCTA-AAATGTAATTTAT-AGAAAATTTA
* * *
5369567 GGGGGTGAAATGTAATTTCA-A-AAAGTTTA
1 GGGGCTAAAATGTAATTT-ATAGAAAATTTA
* * *
5369596 GGGGTTGAAATGTAATTTAGA-AAAATTTA
1 GGGGCTAAAATGTAATTTATAGAAAATTTA
*
5369625 GGGGCCAAAATGTAATTTAT
1 GGGGCTAAAATGTAATTTAT
5369645 GTTTTTTTTG
Statistics
Matches: 138, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.05
29 88 0.64
30 37 0.27
31 6 0.04
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (30 bp):
GGGGCTAAAATGTAATTTATAGAAAATTTA
Found at i:5369519 original size:30 final size:29
Alignment explanation
Indices: 5369485--5369644 Score: 162
Period size: 29 Copynumber: 5.4 Consensus size: 29
5369475 TATGGGGCTA
*
5369485 AAATGTAATTTATAGAAAGTTTAGGGGCCC
1 AAATGTAATTTATA-AAAGTTTAGGGGCCG
* * **
5369515 AAATGCAATTTAGAAAAGTTTAGGGGTAG
1 AAATGTAATTTATAAAAGTTTAGGGGCCG
**
5369544 AAATGTAATTT-TGAGAAAGTTTAGGGGGTG
1 AAATGTAATTTAT-A-AAAGTTTAGGGGCCG
**
5369574 AAATGTAATTTCA-AAAAGTTTAGGGGTTG
1 AAATGTAATTT-ATAAAAGTTTAGGGGCCG
* * *
5369603 AAATGTAATTTAGAAAAATTTAGGGGCCA
1 AAATGTAATTTATAAAAGTTTAGGGGCCG
5369632 AAATGTAATTTAT
1 AAATGTAATTTAT
5369645 GTTTTTTTTG
Statistics
Matches: 110, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.01
29 72 0.65
30 37 0.34
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (29 bp):
AAATGTAATTTATAAAAGTTTAGGGGCCG
Found at i:5369548 original size:59 final size:58
Alignment explanation
Indices: 5369485--5369643 Score: 205
Period size: 59 Copynumber: 2.7 Consensus size: 58
5369475 TATGGGGCTA
* *
5369485 AAATGTAATTTATAGAAAGTTTAGGGGCCCAAATGCAATTTAGAAAAGTTTAGGGGTAG
1 AAATGTAATTTATAGAAAGTTTAGGGGCCAAAATGTAATTTA-AAAAGTTTAGGGGTAG
*** *
5369544 AAATGTAATTT-TGAGAAAGTTTAGGGGGTGAAATGTAATTTCAAAAAGTTTAGGGGTTG
1 AAATGTAATTTAT-AGAAAGTTTAGGGGCCAAAATGTAATTT-AAAAAGTTTAGGGGTAG
* *
5369603 AAATGTAATTTAGA-AAAATTTAGGGGCCAAAATGTAATTTA
1 AAATGTAATTTATAGAAAGTTTAGGGGCCAAAATGTAATTTA
5369644 TGTTTTTTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
57 1 0.01
58 23 0.26
59 62 0.71
60 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (58 bp):
AAATGTAATTTATAGAAAGTTTAGGGGCCAAAATGTAATTTAAAAAGTTTAGGGGTAG
Found at i:5371410 original size:79 final size:79
Alignment explanation
Indices: 5371320--5371556 Score: 465
Period size: 79 Copynumber: 3.0 Consensus size: 79
5371310 TTGTGTGCGT
5371320 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
1 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
5371385 GGTGGAGTTCTTTA
66 GGTGGAGTTCTTTA
5371399 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
1 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
5371464 GGTGGAGTTCTTTA
66 GGTGGAGTTCTTTA
5371478 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
1 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
*
5371543 GGAGGAGTTCTTTA
66 GGTGGAGTTCTTTA
5371557 GGAATCCTCA
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 157 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.49
Consensus pattern (79 bp):
TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
GGTGGAGTTCTTTA
Found at i:5395039 original size:56 final size:56
Alignment explanation
Indices: 5394970--5395147 Score: 356
Period size: 56 Copynumber: 3.2 Consensus size: 56
5394960 ACCAAGAAGA
5394970 GGTTGATTGATTGTTCGTGGTCACTTATTTCTCAAGTAGAGAATCAAGTCAGAGTT
1 GGTTGATTGATTGTTCGTGGTCACTTATTTCTCAAGTAGAGAATCAAGTCAGAGTT
5395026 GGTTGATTGATTGTTCGTGGTCACTTATTTCTCAAGTAGAGAATCAAGTCAGAGTT
1 GGTTGATTGATTGTTCGTGGTCACTTATTTCTCAAGTAGAGAATCAAGTCAGAGTT
5395082 GGTTGATTGATTGTTCGTGGTCACTTATTTCTCAAGTAGAGAATCAAGTCAGAGTT
1 GGTTGATTGATTGTTCGTGGTCACTTATTTCTCAAGTAGAGAATCAAGTCAGAGTT
5395138 GGTTGATTGA
1 GGTTGATTGA
5395148 CAGTGGTTGC
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 122 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.38
Consensus pattern (56 bp):
GGTTGATTGATTGTTCGTGGTCACTTATTTCTCAAGTAGAGAATCAAGTCAGAGTT
Found at i:5405307 original size:30 final size:30
Alignment explanation
Indices: 5405273--5405335 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
5405263 ACTTATTATA
5405273 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
5405303 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
5405333 TTG
1 TTG
5405336 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Done.