Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 8 of 54
Found at i:3750334 original size:83 final size:84
Alignment explanation
Indices: 3750222--3750395 Score: 242
Period size: 84 Copynumber: 2.1 Consensus size: 84
3750212 GCATAAAGTA
* * * * *
3750222 AAATCATTCTCATGCTTAGCCTATAGTGTATATGA-ATTCTCAGCGCATACATCTCATGGCATAC
1 AAATCATTCTCATGCCTAGCCCATAGTGTACATGATATTCTCAACACATACATCTCATGGCATAC
* *
3750286 ATTTTATATTTTATCTCAT
66 ATTTCATATCTTATCTCAT
* * * *
3750305 AAATTATTCTCGTGCCTAGCCCATGGTGTACATGATATTCTCAACACATACATCTTATGGCATAC
1 AAATCATTCTCATGCCTAGCCCATAGTGTACATGATATTCTCAACACATACATCTCATGGCATAC
3750370 ATTTCATATCTTATCTCAT
66 ATTTCATATCTTATCTCAT
3750389 AAATCAT
1 AAATCAT
3750396 CATCATATCA
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
83 29 0.37
84 49 0.63
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (84 bp):
AAATCATTCTCATGCCTAGCCCATAGTGTACATGATATTCTCAACACATACATCTCATGGCATAC
ATTTCATATCTTATCTCAT
Found at i:3753691 original size:15 final size:16
Alignment explanation
Indices: 3753660--3753702 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
3753650 TTATTTTATG
3753660 TTAACATTATAAAAATTA
1 TTAAC-TTAT-AAAATTA
3753678 -TAACTTATAAAATTA
1 TTAACTTATAAAATTA
3753693 TTAA-TTATAA
1 TTAACTTATAA
3753703 TATACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAACTTATAAAATTA
Found at i:3753708 original size:344 final size:342
Alignment explanation
Indices: 3753068--3753706 Score: 955
Period size: 344 Copynumber: 1.9 Consensus size: 342
3753058 AAAGAGTCTT
3753068 TGAGATTAGAATAGTTTTGGAATATAACTATTTTTTTAATTTCATGTAATTAAAGACAAACCCAT
1 TGAGATTAGAATAGTTTTGGAATATAACTATTTTTTTAATTTCATGTAATTAAAGACAAACCCAT
* * * *
3753133 ATAGTTAATTAAATTAATTCATTAAACTATGATTATTAATTAACTTAGAATGTTTTTTAATATAT
66 ATAATTAATTAAATTAATTAATGAAACTATGATTATTAATTAACTTAGAATGTCTTTTAATATAT
* *
3753198 ACATTGTATATATTGGGTTCATTTATAAGAAATATAATTACTATATTATATATATATACTAATAC
131 ACATTATATATATTGGGTTCATTTATAAGAAATATAATTA-TATATTATATATATACACTAATAC
* *
3753263 TTTTAGTATTTATATACTTTAAATATAATATATTTACTTTCTATTTTATATTAACATTACAAAAA
195 TTTTAATATATATATACTTTAAATATAATATATTTACTTTCTATTTTATATTAACATTACAAAAA
*
3753328 TTATTAAATTGTAAAATTATTAATTAAAATATATACACCTTTATTTATATAAACTTATAATATAC
260 TTATTAAATTATAAAATTATTAATTAAAATATATACACCTTTATTTATATAAACTTATAATATAC
3753393 AAACCTTAAAAGAAGTTG
325 AAACCTTAAAAGAAGTTG
* * * *
3753411 TGAGATTAGAATAGTTTTGAGACCT-T-ATTATTTTTTTTAATTTCATGTAATTAAGGACAAACT
1 TGAGATTAGAATAGTTTTG-GA-ATATAACTA-TTTTTTTAATTTCATGTAATTAAAGACAAACC
3753474 CATATAATTAATTAAATTAATTAATGAAACTATGATTATTAATTAACTT-GTAATGTCTTTTAAT
63 CATATAATTAATTAAATTAATTAATGAAACTATGATTATTAATTAACTTAG-AATGTCTTTTAAT
* * *
3753538 ATCTATACTTTATATATATTGGGTTCATTTATAAGGAATATAATT-TCTATTATATATATACACT
127 A--TATACATTATATATATTGGGTTCATTTATAAGAAATATAATTATATATTATATATATACACT
* * *
3753602 AAAATACTTTTAATATATATATTCTTTAAATATAAATATATTTACTTTTTATTTTATGTTAACAT
190 --AATACTTTTAATATATATATACTTTAAATAT-AATATATTTACTTTCTATTTTATATTAACAT
* * *
3753667 TATAAAAATTA-TAACTTATAAAATTATTAATTATAATATA
252 TACAAAAATTATTAAATTATAAAATTATTAATTAAAATATA
3753707 CATATATACA
Statistics
Matches: 265, Mismatches: 22, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
343 23 0.09
344 109 0.41
345 1 0.00
346 93 0.35
347 39 0.15
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.45
Consensus pattern (342 bp):
TGAGATTAGAATAGTTTTGGAATATAACTATTTTTTTAATTTCATGTAATTAAAGACAAACCCAT
ATAATTAATTAAATTAATTAATGAAACTATGATTATTAATTAACTTAGAATGTCTTTTAATATAT
ACATTATATATATTGGGTTCATTTATAAGAAATATAATTATATATTATATATATACACTAATACT
TTTAATATATATATACTTTAAATATAATATATTTACTTTCTATTTTATATTAACATTACAAAAAT
TATTAAATTATAAAATTATTAATTAAAATATATACACCTTTATTTATATAAACTTATAATATACA
AACCTTAAAAGAAGTTG
Found at i:3755641 original size:29 final size:24
Alignment explanation
Indices: 3755585--3755639 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
3755575 CATAATTAGA
3755585 TATTGTAGTTTAATTAAATAATGG
1 TATTGTAGTTTAATTAAATAATGG
3755609 TATTGTAGTTTAATTAAATAATGG
1 TATTGTAGTTTAATTAAATAATGG
3755633 TATTGTA
1 TATTGTA
3755640 TTAAAACTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.47
Consensus pattern (24 bp):
TATTGTAGTTTAATTAAATAATGG
Found at i:3761208 original size:31 final size:32
Alignment explanation
Indices: 3761151--3761215 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3761141 AATACAGAAT
3761151 TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
1 TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
3761183 TCCCCTGCGTTACTCAAG-GGAATTTTCAAAG
1 TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
3761214 TC
1 TC
3761216 TGCAGTTGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (32 bp):
TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
Found at i:3765921 original size:20 final size:20
Alignment explanation
Indices: 3765896--3765942 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3765886 TATAATTAGG
3765896 TTAATTTTAAGTTAGTTATT
1 TTAATTTTAAGTTAGTTATT
* * *
3765916 TTAATTTTATGTTATTTCTT
1 TTAATTTTAAGTTAGTTATT
3765936 TTAATTT
1 TTAATTT
3765943 GTTTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (20 bp):
TTAATTTTAAGTTAGTTATT
Found at i:3772793 original size:3 final size:3
Alignment explanation
Indices: 3772761--3772830 Score: 69
Period size: 3 Copynumber: 24.7 Consensus size: 3
3772751 CAGTTTTGGT
* * *
3772761 TTA TT- TTA TT- TTA TTT TTA TTA TT- TCA TTA TTA TT- TTA CT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3772804 TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TT
3772831 CTTTTCCCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
2 8 0.15
3 44 0.80
4 3 0.05
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3772795 original size:30 final size:31
Alignment explanation
Indices: 3772761--3772825 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
3772751 CAGTTTTGGT
* *
3772761 TTATTTTATTTTATTTTTATTATT-TCATTA
1 TTATTTTACTTTATTATTATTATTATCATTA
*
3772791 TTATTTTACTTTATTATTATTATTATTATTA
1 TTATTTTACTTTATTATTATTATTATCATTA
3772822 TTAT
1 TTAT
3772826 CTATTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (31 bp):
TTATTTTACTTTATTATTATTATTATCATTA
Found at i:3772797 original size:25 final size:28
Alignment explanation
Indices: 3772766--3772823 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
3772756 TTGGTTTATT
3772766 TTATTTTA-TTT-TTATTATT-TCATTA
1 TTATTTTACTTTATTATTATTATCATTA
*
3772791 TTATTTTACTTTATTATTATTATTATTA
1 TTATTTTACTTTATTATTATTATCATTA
3772819 TTATT
1 TTATT
3772824 ATCTATTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 8 0.28
26 3 0.10
27 8 0.28
28 10 0.34
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (28 bp):
TTATTTTACTTTATTATTATTATCATTA
Found at i:3774354 original size:20 final size:20
Alignment explanation
Indices: 3774325--3774367 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3774315 ATTAGGTTAC
3774325 TTTTAAGTTAGTTATTTTAA
1 TTTTAAGTTAGTTATTTTAA
* * *
3774345 TTTTATGTTATTTCTTTTAA
1 TTTTAAGTTAGTTATTTTAA
3774365 TTT
1 TTT
3774368 GTTTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTAAGTTAGTTATTTTAA
Found at i:3781564 original size:30 final size:30
Alignment explanation
Indices: 3781523--3781579 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
3781513 CTGTAAAGTG
*
3781523 TAGCTGTTTCTAGGAACTCATGAGCTTGTC
1 TAGCCGTTTCTAGGAACTCATGAGCTTGTC
3781553 TAGCCGTTTCTAGGAACTCATGAGCTT
1 TAGCCGTTTCTAGGAACTCATGAGCTT
3781580 AGTTGTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (30 bp):
TAGCCGTTTCTAGGAACTCATGAGCTTGTC
Found at i:3792026 original size:38 final size:39
Alignment explanation
Indices: 3791919--3792114 Score: 205
Period size: 39 Copynumber: 5.0 Consensus size: 39
3791909 TTATTTTCTT
* * **
3791919 TTTTGGTATGTATTCATATGACGAAGAATGATTTACAAATG
1 TTTTGGT-T-TATTCATATGATGAAGATTGATTTATGAATG
* *
3791960 TTTTTGTTCATTCATATGATGAAGATTGA-TTATGAATG
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
* * * * *
3791998 CTTTGGTTTATTCATATGTTAAAAATTGATTTATGAAAG
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
* **
3792037 TTTTGGTTTATTAATATGATGAAGATTGATTTACAAATG
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
* * * *
3792076 TTTTGGTTTACTCATATGATGAATACTGATTGATGAATG
1 TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
3792115 AGATGAAATC
Statistics
Matches: 126, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
38 30 0.24
39 89 0.71
40 1 0.01
41 6 0.05
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (39 bp):
TTTTGGTTTATTCATATGATGAAGATTGATTTATGAATG
Found at i:3793770 original size:83 final size:84
Alignment explanation
Indices: 3793671--3793836 Score: 262
Period size: 84 Copynumber: 2.0 Consensus size: 84
3793661 TGTCATAATT
* * * *
3793671 CATTCTCATGCTTAGCCTATAGTGTATATGA-ATTCTCAATACATACATCTCATGGCATACATTT
1 CATTCTCATGCCTAGCCCATAGTGTACATGATATTCTCAACACATACATCTCATGGCATACATTT
*
3793735 CATATTTTATCTCATAAAC
66 CATATCTTATCTCATAAAC
* *
3793754 CATTCTTATGCCTAGCCCATAGTGTACATGATATTTTCAACACATACATCTCATGGCATACATTT
1 CATTCTCATGCCTAGCCCATAGTGTACATGATATTCTCAACACATACATCTCATGGCATACATTT
3793819 CATATCTTATCTCATAAA
66 CATATCTTATCTCATAAA
3793837 TCATCATCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
83 27 0.36
84 48 0.64
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.37
Consensus pattern (84 bp):
CATTCTCATGCCTAGCCCATAGTGTACATGATATTCTCAACACATACATCTCATGGCATACATTT
CATATCTTATCTCATAAAC
Found at i:3801910 original size:31 final size:32
Alignment explanation
Indices: 3801853--3801917 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3801843 AACAATGAAT
3801853 TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
1 TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
3801885 TCCCCTGCGTTACTCAAG-GGAATTTTCAAAG
1 TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
3801916 TC
1 TC
3801918 TGCAGTTGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (32 bp):
TCCCCTGCGTTACTCAAGCGGAATTTTCAAAG
Found at i:3817586 original size:17 final size:19
Alignment explanation
Indices: 3817564--3817598 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3817554 CCAAGTGACC
3817564 ATGG-AAATT-TTCTATAA
1 ATGGAAAATTCTTCTATAA
3817581 ATGGAAAATTCTTCTATA
1 ATGGAAAATTCTTCTATA
3817599 GCAACTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (19 bp):
ATGGAAAATTCTTCTATAA
Found at i:3859847 original size:24 final size:23
Alignment explanation
Indices: 3859807--3859852 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3859797 TATTGAAAAA
*
3859807 AAATAAAAAAGAAATAATTTTTT
1 AAATAAAAAAGAAATAAATTTTT
*
3859830 AAATAAAAAAGAGTATAAATTTT
1 AAATAAAAAAGA-AATAAATTTT
3859853 ATTAGTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
AAATAAAAAAGAAATAAATTTTT
Found at i:3860020 original size:21 final size:20
Alignment explanation
Indices: 3859996--3860042 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
3859986 GCAGTTGCAA
3859996 TTAATTATATAA-TAAATTGTT
1 TTAATTATA-AACTAAATT-TT
*
3860017 TTAATT-TAAACTTAATTTT
1 TTAATTATAAACTAAATTTT
3860036 TTAATTA
1 TTAATTA
3860043 AAGTAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 6 0.26
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATTATAAACTAAATTTT
Found at i:3860737 original size:59 final size:59
Alignment explanation
Indices: 3860671--3860864 Score: 343
Period size: 59 Copynumber: 3.3 Consensus size: 59
3860661 TCTGTGCTTT
3860671 CAATGCTTAAAATGACCTGAGTTGCCACCTTTGAAGAATTTCTATCATTTCAAGGATTG
1 CAATGCTTAAAATGACCTGAGTTGCCACCTTTGAAGAATTTCTATCATTTCAAGGATTG
3860730 CAATGCTTAAAATGACCTGAGTTGCCACCTTTGAAGAATTTCTATCATTTCAAGGATTG
1 CAATGCTTAAAATGACCTGAGTTGCCACCTTTGAAGAATTTCTATCATTTCAAGGATTG
** *
3860789 CAATGCTTAAAATGACCTGAGTTGCCAATTTTGAAGAATTTCTATCATTTCAAGGATTT
1 CAATGCTTAAAATGACCTGAGTTGCCACCTTTGAAGAATTTCTATCATTTCAAGGATTG
**
3860848 CAATGCTTTGAATGACC
1 CAATGCTTAAAATGACC
3860865 CTGTCCTGTT
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 130 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (59 bp):
CAATGCTTAAAATGACCTGAGTTGCCACCTTTGAAGAATTTCTATCATTTCAAGGATTG
Found at i:3866471 original size:31 final size:31
Alignment explanation
Indices: 3866433--3866494 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3866423 AAATATGGAT
3866433 TTGATGCTGAGACTATGTTCTCAACATGGTG
1 TTGATGCTGAGACTATGTTCTCAACATGGTG
3866464 TTGATGCTGAGACTATGTTCTCAACATGGTG
1 TTGATGCTGAGACTATGTTCTCAACATGGTG
3866495 GTAGCCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (31 bp):
TTGATGCTGAGACTATGTTCTCAACATGGTG
Found at i:3866545 original size:34 final size:34
Alignment explanation
Indices: 3866507--3866574 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
3866497 AGCCTTATCA
*
3866507 CTTTAAGCTTACATGTTTTTAATTCTTCTTTTCT
1 CTTTAAGCTTACAAGTTTTTAATTCTTCTTTTCT
*
3866541 CTTTAAGCTTACAAGTTTTTAGTTCTTCTTTTCT
1 CTTTAAGCTTACAAGTTTTTAATTCTTCTTTTCT
3866575 ATTATCCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.57
Consensus pattern (34 bp):
CTTTAAGCTTACAAGTTTTTAATTCTTCTTTTCT
Found at i:3870339 original size:2 final size:2
Alignment explanation
Indices: 3870334--3870370 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3870324 CTTAAAAAAA
3870334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3870371 GATAGTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3871639 original size:8 final size:8
Alignment explanation
Indices: 3871628--3871665 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
3871618 TATATTAATA
3871628 AATTATAG
1 AATTATAG
3871636 AATTATAG
1 AATTATAG
*
3871644 AATTATTG
1 AATTATAG
3871652 AATTATAG
1 AATTATAG
3871660 AATTAT
1 AATTAT
3871666 GCATTGTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (8 bp):
AATTATAG
Found at i:3872387 original size:35 final size:33
Alignment explanation
Indices: 3872347--3872433 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
3872337 TTTTAATATC
* *
3872347 ATATATTTTATTGTT-ATTTCTTATTATAATCTT
1 ATATATATTATT-TTCATTTCTTAATATAATCTT
*
3872380 ATATATATTATTTTCATTTCTTAATATAATTTT
1 ATATATATTATTTTCATTTCTTAATATAATCTT
* *
3872413 TTATATTATATATTTTAATTT
1 ATATA-TAT-TATTTTCATTT
3872434 AATTTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.04
33 31 0.67
34 3 0.07
35 10 0.22
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (33 bp):
ATATATATTATTTTCATTTCTTAATATAATCTT
Found at i:3955921 original size:19 final size:19
Alignment explanation
Indices: 3955897--3955951 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
3955887 ATTTGACTCA
*
3955897 TTAGTTGGTGTATGATCTT
1 TTAGTTGGTGCATGATCTT
3955916 TTAGTTGGTGCATGATCTT
1 TTAGTTGGTGCATGATCTT
3955935 TTAGTTGGTGCATGATC
1 TTAGTTGGTGCATGATC
3955952 CCTCGTCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.47
Consensus pattern (19 bp):
TTAGTTGGTGCATGATCTT
Found at i:3959927 original size:53 final size:53
Alignment explanation
Indices: 3959846--3959969 Score: 155
Period size: 53 Copynumber: 2.3 Consensus size: 53
3959836 GATTAACTGC
* * *
3959846 ACTCTTAGTTGGCTAAGTTGTCTCTGTCTTCTAA-TCCTAG-TTTTTGGCAAT-G
1 ACTCTTAGTCGACTAAGTTGTCTCTGTCTT-GAAGTCC-AGATTTTTGGCAATAG
* *
3959898 AGCTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCCAGATTTTTGGCAATAG
1 A-CTCTTAGTCGACTAAGTTGTCTCTGTCTTGAAGTCCAGATTTTTGGCAATAG
3959952 ACTCTTAGTCGACTAAGT
1 ACTCTTAGTCGACTAAGT
3959970 CTTCTTTGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
52 5 0.08
53 55 0.89
54 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (53 bp):
ACTCTTAGTCGACTAAGTTGTCTCTGTCTTGAAGTCCAGATTTTTGGCAATAG
Found at i:3964034 original size:65 final size:65
Alignment explanation
Indices: 3963928--3964127 Score: 260
Period size: 65 Copynumber: 3.0 Consensus size: 65
3963918 TCCTTTCATT
*
3963928 TTGGAATTATTTTTTGTATGTACAAACCATTGAAAAGAAAGATTGAATTTAAAACATGCTAAAAC
1 TTGGAATTA--TTTTGTATGTACAAACCGTTGAAAAGAAAGATTGAATTTAAAACATGCTAAAAC
3963993 TA
64 TA
3963995 TTGGAATTATTTTGTATGTACAAACCGTTGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTA
1 TTGGAATTATTTTGTATGTACAAACCGTTGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTA
* * ** * ** *
3964060 TT-AAATTGTGATGAACCTGTA-AATAATGGTGAAAAGAAAGATTGAATTTAAAACATGCTAAAA
1 TTGGAATTATTTTGTA--TGTACAA-ACCGTTGAAAAGAAAGATTGAATTTAAAACATGCTAAAA
3964123 CTA
63 CTA
3964126 TT
1 TT
3964128 AAATTGTGAT
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
64 8 0.07
65 59 0.49
66 45 0.37
67 9 0.07
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.33
Consensus pattern (65 bp):
TTGGAATTATTTTGTATGTACAAACCGTTGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTA
Found at i:3964129 original size:66 final size:65
Alignment explanation
Indices: 3963958--3964156 Score: 276
Period size: 66 Copynumber: 3.0 Consensus size: 65
3963948 TACAAACCAT
* * ** * **
3963958 TGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTATTGGAATTATTTTGTA-TGTACAA-ACC
1 TGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTATT-AAATTGTGATGAACTGTA-AATAAT
*
3964021 GT
64 GG
3964023 TGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTATTAAATTGTGATGAACCTGTAAATAATG
1 TGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTATTAAATTGTGATGAA-CTGTAAATAATG
3964088 G
65 G
3964089 TGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTATTAAATTGTGATGAACGTGTAAATAATG
1 TGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTATTAAATTGTGATGAAC-TGTAAATAATG
3964154 G
65 G
3964155 TG
1 TG
3964157 CTAATTTTGC
Statistics
Matches: 122, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
64 8 0.07
65 42 0.34
66 72 0.59
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (65 bp):
TGAAAAGAAAGATTGAATTTAAAACATGCTAAAACTATTAAATTGTGATGAACTGTAAATAATGG
Found at i:3980603 original size:30 final size:30
Alignment explanation
Indices: 3980569--3980648 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
3980559 CACGAACTAG
3980569 TAATTATAATTAAATAAATAAATTATT-ATT
1 TAATTATAATTAAATAAATAAA-TATTAATT
*
3980599 TAATTATAATTGTAAGTAAA-AAATATTAATT
1 TAATTATAA-T-TAAATAAATAAATATTAATT
* *
3980630 TAATTTTAATTAATTAAAT
1 TAATTATAATTAAATAAAT
3980649 TAAAACAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
29 7 0.16
30 14 0.33
31 15 0.35
32 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (30 bp):
TAATTATAATTAAATAAATAAATATTAATT
Found at i:3998669 original size:26 final size:28
Alignment explanation
Indices: 3998638--3998700 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 28
3998628 TGCCAAAGCG
*
3998638 CTTTTTC-CATGGCAATAATGCACTTCT
1 CTTTTTCGCAAGGCAATAATGCACTTCT
3998665 CTTTTGATCTGCAAGGCAATAATGCACTTCT
1 CTTTT--TC-GCAAGGCAATAATGCACTTCT
3998696 CTTTT
1 CTTTT
3998701 GATCTGCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.16
29 2 0.06
31 24 0.77
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (28 bp):
CTTTTTCGCAAGGCAATAATGCACTTCT
Found at i:3998683 original size:31 final size:31
Alignment explanation
Indices: 3998648--3998709 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3998638 CTTTTTCCAT
3998648 GGCAATAATGCACTTCTCTTTTGATCTGCAA
1 GGCAATAATGCACTTCTCTTTTGATCTGCAA
3998679 GGCAATAATGCACTTCTCTTTTGATCTGCAA
1 GGCAATAATGCACTTCTCTTTTGATCTGCAA
3998710 ACCATCGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (31 bp):
GGCAATAATGCACTTCTCTTTTGATCTGCAA
Found at i:4003642 original size:74 final size:75
Alignment explanation
Indices: 4003492--4003648 Score: 219
Period size: 74 Copynumber: 2.1 Consensus size: 75
4003482 TGACGGATTG
* *
4003492 TGCCAGACTTATCATGTCAGCTGCAAACGAATACTCCATGATTGACAAAAACATCAAAATGGGAA
1 TGCCAGAGTTATCATATCAGCTGCAAACGAATACTCCATGATTGACAAAAACATCAAAATGGGAA
*
4003557 AGAAAGGGCT
66 AGAAAAGGCT
* * * *
4003567 TGCCAGAGTTATCATATCAGCTGCAAATGTGA-ACTCCAT-ATTGATAAAAACATGAAAATGGGA
1 TGCCAGAGTTATCATATCAGCTGCAAACG-AATACTCCATGATTGACAAAAACATCAAAATGGGA
*
4003630 AAGAAAATGCT
65 AAGAAAAGGCT
4003641 TGCCAGAG
1 TGCCAGAG
4003649 ATCTCGTCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
74 39 0.53
75 33 0.45
76 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (75 bp):
TGCCAGAGTTATCATATCAGCTGCAAACGAATACTCCATGATTGACAAAAACATCAAAATGGGAA
AGAAAAGGCT
Found at i:4015929 original size:2 final size:2
Alignment explanation
Indices: 4015924--4015954 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4015914 CAGCACTAGG
4015924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4015955 ATNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4016330 original size:2 final size:2
Alignment explanation
Indices: 4016325--4016359 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4016315 CAGCACTAAG
4016325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4016360 GAAGATATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4018670 original size:25 final size:26
Alignment explanation
Indices: 4018636--4018685 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
4018626 TCCAACTTTT
4018636 AATAAAATATTAATA-TTAAATTATA
1 AATAAAATATTAATATTTAAATTATA
4018661 AATAAAATATTAATATTTAAATTAT
1 AATAAAATATTAATATTTAAATTAT
4018686 CAATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAAATATTAATATTTAAATTATA
Found at i:4021349 original size:12 final size:11
Alignment explanation
Indices: 4021289--4021349 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 11
4021279 CCCATAAAAG
4021289 GAAAAG-AGAAA
1 GAAAAGAAG-AA
*
4021300 GAAAAGCAG-A
1 GAAAAGAAGAA
4021310 GAAAAGAAGAAA
1 GAAAAGAAG-AA
4021322 GAAAAGCAGAGAA
1 GAAAAG-A-AGAA
4021335 GAAAAGAATGAA
1 GAAAAGAA-GAA
4021347 GAA
1 GAA
4021350 GTGTGAGCTG
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
10 9 0.21
11 7 0.16
12 16 0.37
13 9 0.21
14 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.28, T:0.02
Consensus pattern (11 bp):
GAAAAGAAGAA
Found at i:4021349 original size:25 final size:22
Alignment explanation
Indices: 4021289--4021342 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
4021279 CCCATAAAAG
4021289 GAAAAG-AGAAAGAAAAGCAGA
1 GAAAAGAAGAAAGAAAAGCAGA
4021310 GAAAAGAAGAAAGAAAAGCAGA
1 GAAAAGAAGAAAGAAAAGCAGA
4021332 GAAGAA-AAGAA
1 GAA-AAGAAGAA
4021343 TGAAGAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.19
22 23 0.74
23 2 0.06
ACGTcount: A:0.69, C:0.04, G:0.28, T:0.00
Consensus pattern (22 bp):
GAAAAGAAGAAAGAAAAGCAGA
Found at i:4021656 original size:3 final size:3
Alignment explanation
Indices: 4021648--4021673 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4021638 TGAAGACGAT
4021648 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
4021674 TCATGAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4021687 original size:3 final size:3
Alignment explanation
Indices: 4021681--4021720 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
4021671 AGATCATGAA
* * *
4021681 GAG GAG GAG GAG GAG GAG GAA GAG GAA GAG GAA GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
4021721 TTGAAGATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:4021696 original size:12 final size:12
Alignment explanation
Indices: 4021681--4021720 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
4021671 AGATCATGAA
*
4021681 GAGGAGGAGGAG
1 GAGGAGGAAGAG
4021693 GAGGAGGAAGAG
1 GAGGAGGAAGAG
*
4021705 GAAGAGGAAGAG
1 GAGGAGGAAGAG
4021717 GAGG
1 GAGG
4021721 TTGAAGATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (12 bp):
GAGGAGGAAGAG
Found at i:4028952 original size:29 final size:30
Alignment explanation
Indices: 4028907--4028964 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
4028897 GTTTTTTGAC
4028907 AAAAAAGGATAACGAACAATCATATCAAGA
1 AAAAAAGGATAACGAACAATCATATCAAGA
*
4028937 AAAAAAGG-TAATGAACAATCATATCAAG
1 AAAAAAGGATAACGAACAATCATATCAAG
4028965 TGACTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.16
Consensus pattern (30 bp):
AAAAAAGGATAACGAACAATCATATCAAGA
Found at i:4032822 original size:5 final size:5
Alignment explanation
Indices: 4032812--4032840 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4032802 AGAGAAAATT
4032812 TTTAA TTTAA TTTAA TTTAA TTT-A TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
4032841 AAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:4035895 original size:2 final size:2
Alignment explanation
Indices: 4035890--4035918 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4035880 GTTGTGTGTG
4035890 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4035919 GGACTATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4052772 original size:15 final size:14
Alignment explanation
Indices: 4052762--4052794 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4052752 CCTCTTTCTT
4052762 TTTTTATTCTTTTA
1 TTTTTATTCTTTTA
4052776 TTTTTATT-TTTTA
1 TTTTTATTCTTTTA
*
4052789 TATTTA
1 TTTTTA
4052795 ACAATGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTCTTTTA
Found at i:4059651 original size:17 final size:17
Alignment explanation
Indices: 4059621--4059662 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4059611 TTACTGTCTT
*
4059621 CCATC-TTTGGTTTTAA
1 CCATCTTTTGATTTTAA
* *
4059637 CCTTCTTTTGATTTTTA
1 CCATCTTTTGATTTTAA
4059654 CCATCTTTT
1 CCATCTTTT
4059663 ATTACAGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (17 bp):
CCATCTTTTGATTTTAA
Found at i:4066588 original size:22 final size:23
Alignment explanation
Indices: 4066563--4066609 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
4066553 TAATTAGAAG
4066563 CCAATAC-CTCCCAATTTAAGTT
1 CCAATACGCTCCCAATTTAAGTT
*
4066585 CCAATACTGGCTCCTAATTTAAGTT
1 CCAATAC--GCTCCCAATTTAAGTT
4066610 GCATTACTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
25 14 0.67
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.34
Consensus pattern (23 bp):
CCAATACGCTCCCAATTTAAGTT
Found at i:4066603 original size:25 final size:25
Alignment explanation
Indices: 4066570--4066624 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
4066560 AAGCCAATAC
*
4066570 CTCCCAATTTAAGTTCCAATACTGG
1 CTCCTAATTTAAGTTCCAATACTGG
* *
4066595 CTCCTAATTTAAGTTGCATTACTGG
1 CTCCTAATTTAAGTTCCAATACTGG
4066620 CTCCT
1 CTCCT
4066625 GTTCTTGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (25 bp):
CTCCTAATTTAAGTTCCAATACTGG
Found at i:4067272 original size:2 final size:2
Alignment explanation
Indices: 4067267--4067298 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4067257 TTTACTACGT
*
4067267 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4067299 CATGTGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4068443 original size:29 final size:30
Alignment explanation
Indices: 4068397--4068453 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
4068387 CAAGAGAATG
4068397 ACTTGAACCCCAATTAGGTTCTATTAATCT
1 ACTTGAACCCCAATTAGGTTCTATTAATCT
4068427 ACTTGAA-CCCAATTAGGTTCTATTAAT
1 ACTTGAACCCCAATTAGGTTCTATTAAT
4068454 TAGGTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (30 bp):
ACTTGAACCCCAATTAGGTTCTATTAATCT
Found at i:4071739 original size:13 final size:13
Alignment explanation
Indices: 4071721--4071745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4071711 ATTTTGATCG
4071721 AAAAAATTTCAAT
1 AAAAAATTTCAAT
4071734 AAAAAATTTCAA
1 AAAAAATTTCAA
4071746 CTTATTAATA
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATTTCAAT
Found at i:4083648 original size:21 final size:21
Alignment explanation
Indices: 4083622--4083661 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4083612 TAAGTTGAGG
*
4083622 GAGGAGAAGAGGAGGAAAGCT
1 GAGGAGAAAAGGAGGAAAGCT
*
4083643 GAGGAGAAAATGAGGAAAG
1 GAGGAGAAAAGGAGGAAAG
4083662 TCATGGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.45, T:0.05
Consensus pattern (21 bp):
GAGGAGAAAAGGAGGAAAGCT
Found at i:4087285 original size:24 final size:24
Alignment explanation
Indices: 4087258--4087355 Score: 74
Period size: 24 Copynumber: 4.1 Consensus size: 24
4087248 TGTTACACAT
4087258 CATAGACAAAAACATATGACACGC
1 CATAGACAAAAACATATGACACGC
* * * *
4087282 CATATACAGAAACATATAACACGT
1 CATAGACAAAAACATATGACACGC
* * * * *
4087306 TATATACAGAAACATGTGACATGC
1 CATAGACAAAAACATATGACACGC
* *
4087330 TAT-GTA-AAAAAAATATGACACGC
1 CATAG-ACAAAAACATATGACACGC
4087353 CAT
1 CAT
4087356 GGTTAGGTTG
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
23 15 0.26
24 43 0.74
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.20
Consensus pattern (24 bp):
CATAGACAAAAACATATGACACGC
Found at i:4099567 original size:51 final size:51
Alignment explanation
Indices: 4099491--4099591 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
4099481 CCGTTACAAG
4099491 TGGTATCGGAGTAAATCTAAATCTTCACTGATGTAGGACTCTCATGAGAGT
1 TGGTATCGGAGTAAATCTAAATCTTCACTGATGTAGGACTCTCATGAGAGT
*
4099542 TGGTATCGGAGTAGATCTAAATCTTCACTGATGTAGGACTCTCATGAGAG
1 TGGTATCGGAGTAAATCTAAATCTTCACTGATGTAGGACTCTCATGAGAG
4099592 ATAGAAGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (51 bp):
TGGTATCGGAGTAAATCTAAATCTTCACTGATGTAGGACTCTCATGAGAGT
Found at i:4105069 original size:20 final size:20
Alignment explanation
Indices: 4105031--4105070 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4105021 AAAGTTTAAA
* * *
4105031 TTTTATAATTTTTTCATTTT
1 TTTTAAAATTTTATAATTTT
4105051 TTTTAAAATTTTATAATTTT
1 TTTTAAAATTTTATAATTTT
4105071 ACCTTTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAAAATTTTATAATTTT
Found at i:4105093 original size:14 final size:15
Alignment explanation
Indices: 4105076--4105117 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
4105066 ATTTTACCTT
4105076 TATATATT-TTTTAA
1 TATATATTATTTTAA
4105090 TATA-ATTATTTT-A
1 TATATATTATTTTAA
*
4105103 TAAATATTATTTTAA
1 TATATATTATTTTAA
4105118 CCCATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 7 0.29
14 16 0.67
15 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATATTATTTTAA
Found at i:4109714 original size:54 final size:53
Alignment explanation
Indices: 4109632--4109738 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 53
4109622 ACCATGCCTT
4109632 ATTCAATGAATATAGTGAATGGTTTTCAAGAAGATTAATTCATTGCATCATGAC
1 ATTCAATGAATATAGTGAATGGTTTTCAAGAAGATTAATTCA-TGCATCATGAC
* **
4109686 ATTCAATGGATATAGTGCGTGGTTTTCAAGAAGATTAATTCATGCATCATGAC
1 ATTCAATGAATATAGTGAATGGTTTTCAAGAAGATTAATTCATGCATCATGAC
4109739 TCTTTGAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
53 11 0.22
54 39 0.78
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (53 bp):
ATTCAATGAATATAGTGAATGGTTTTCAAGAAGATTAATTCATGCATCATGAC
Found at i:4120392 original size:23 final size:23
Alignment explanation
Indices: 4120348--4120392 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4120338 TGGATATTTT
* *
4120348 TAAAATTTTTTTATTATTATATA
1 TAAAATTTTTATATTATAATATA
4120371 TAAAATTTTATATATT-TAATAT
1 TAAAATTTT-TATATTATAATAT
4120393 GATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAAATTTTTATATTATAATATA
Found at i:4120679 original size:2 final size:2
Alignment explanation
Indices: 4120672--4120707 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4120662 CATAAATTTC
4120672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4120708 TATCTCAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4126371 original size:34 final size:35
Alignment explanation
Indices: 4126304--4126373 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
4126294 TGCAATCCAA
4126304 GATAAAATATTATTAATCACTCTATATATATAACTT
1 GATAAAATATTATTAATCACTC-ATATATATAACTT
4126340 GATAAAATATTATTAATCACTC-TATATATAACTT
1 GATAAAATATTATTAATCACTCATATATATAACTT
4126374 ACCACAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 12 0.35
36 22 0.65
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.41
Consensus pattern (35 bp):
GATAAAATATTATTAATCACTCATATATATAACTT
Found at i:4141892 original size:2 final size:2
Alignment explanation
Indices: 4141885--4141918 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4141875 AAAAACAGAA
4141885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4141919 GGACTTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4148834 original size:73 final size:73
Alignment explanation
Indices: 4148711--4148854 Score: 270
Period size: 73 Copynumber: 2.0 Consensus size: 73
4148701 TTCAATAAAG
4148711 TTTGGACCATGTTCATTGGCACAGGTTATCAGAAAATTTAAGGAGACAATGCATCTGCAAGACAA
1 TTTGGACCATGTTCATTGGCACAGGTTATCAGAAAATTTAAGGAGACAATGCATCTGCAAGACAA
4148776 TATCTTTT
66 TATCTTTT
* *
4148784 TTTGGACCATGTTCATTGGCACAGGTTATCAGAAAATTTAAGGAGGCAATGCATCTGCAGGACAA
1 TTTGGACCATGTTCATTGGCACAGGTTATCAGAAAATTTAAGGAGACAATGCATCTGCAAGACAA
4148849 TATCTT
66 TATCTT
4148855 GTTGCTCAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (73 bp):
TTTGGACCATGTTCATTGGCACAGGTTATCAGAAAATTTAAGGAGACAATGCATCTGCAAGACAA
TATCTTTT
Found at i:4156383 original size:20 final size:18
Alignment explanation
Indices: 4156355--4156398 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
4156345 TTCATTTGCA
4156355 AAATAATTTAAAAAATTATT
1 AAATAATTT-AAAAATT-TT
*
4156375 AAATTATTTAAAAATTTT
1 AAATAATTTAAAAATTTT
4156393 AAATAA
1 AAATAA
4156399 ACTCTCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATAATTTAAAAATTTT
Found at i:4160397 original size:28 final size:28
Alignment explanation
Indices: 4160365--4160421 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
4160355 TGTCTAATAA
* * *
4160365 TTTTTGTTTTTATGAGA-GGTTAAATTG
1 TTTTTTTTTTTATGAAAGGGTTAAACTG
4160392 TTTTTTTTTTTATGAAAGGGTTAAACTG
1 TTTTTTTTTTTATGAAAGGGTTAAACTG
4160420 TT
1 TT
4160422 AAAGTTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.23, C:0.02, G:0.19, T:0.56
Consensus pattern (28 bp):
TTTTTTTTTTTATGAAAGGGTTAAACTG
Found at i:4163171 original size:55 final size:55
Alignment explanation
Indices: 4163111--4163218 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 55
4163101 ATTCATATCA
* **
4163111 CACATGTATTTTTCGTATATGGATGATTATGTACTTCTTAAATACATGTTCATAG
1 CACATGTATTTTTCATATATCAATGATTATGTACTTCTTAAATACATGTTCATAG
* *
4163166 CACATGTTTTTTTCATATATCAATGATTATGTAGTTCTTAAATACATGTTCAT
1 CACATGTATTTTTCATATATCAATGATTATGTACTTCTTAAATACATGTTCAT
4163219 GATGGCATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (55 bp):
CACATGTATTTTTCATATATCAATGATTATGTACTTCTTAAATACATGTTCATAG
Found at i:4186243 original size:17 final size:17
Alignment explanation
Indices: 4186221--4186255 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4186211 TAAAATATTT
4186221 TAAAAATTCTTAAA-AAA
1 TAAAAATT-TTAAATAAA
4186238 TAAAAATTTTAAATAAA
1 TAAAAATTTTAAATAAA
4186255 T
1 T
4186256 TTTTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATTTTAAATAAA
Found at i:4188125 original size:87 final size:87
Alignment explanation
Indices: 4187979--4188240 Score: 461
Period size: 87 Copynumber: 3.0 Consensus size: 87
4187969 AGCCGTTGGA
*
4187979 TGCAGGCTGTTGAGTATTTCCAGGAGCGGATTTAGCTGCAGCAGCCATGAGAAGAGACTGTTGCT
1 TGCAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTGCAGCAGCCATGAGAAGAGACTGTTGCT
4188044 GTGCTAGCATAGCTAGTTGCTG
66 GTGCTAGCATAGCTAGTTGCTG
4188066 TGCAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTGCAGCAGCCATGAGAAGAGACTGTTGCT
1 TGCAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTGCAGCAGCCATGAGAAGAGACTGTTGCT
4188131 GTGCTAGCATAGCTAGTTGCTG
66 GTGCTAGCATAGCTAGTTGCTG
* ** *
4188153 TGCAGGCAGTTGAGTATTTCCAGGAGCAGATTTAGAAGCAGCAGCCATGAGAAGAGACTGCTGCT
1 TGCAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTGCAGCAGCCATGAGAAGAGACTGTTGCT
* *
4188218 GTGATAGCATAGATAGTTGCTG
66 GTGCTAGCATAGCTAGTTGCTG
4188240 T
1 T
4188241 TGATGCATCG
Statistics
Matches: 168, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 168 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (87 bp):
TGCAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTGCAGCAGCCATGAGAAGAGACTGTTGCT
GTGCTAGCATAGCTAGTTGCTG
Found at i:4194082 original size:13 final size:13
Alignment explanation
Indices: 4194042--4194074 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4194032 ATATAGTATT
4194042 AAAAT-TTTT-AA
1 AAAATGTTTTGAA
4194053 AAAATGTTTTGAA
1 AAAATGTTTTGAA
4194066 AAAATGTTT
1 AAAATGTTT
4194075 GATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (13 bp):
AAAATGTTTTGAA
Found at i:4194096 original size:11 final size:11
Alignment explanation
Indices: 4194080--4194112 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4194070 TGTTTGATTA
4194080 AAAAAATTAAT
1 AAAAAATTAAT
4194091 AAAAAA--AAT
1 AAAAAATTAAT
4194100 AAAAAATTAAT
1 AAAAAATTAAT
4194111 AA
1 AA
4194113 GTTGAGATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAAATTAAT
Found at i:4201900 original size:20 final size:21
Alignment explanation
Indices: 4201867--4201906 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4201857 TTTTGGGCCT
4201867 CTAATTGACCTGTATATGCAA
1 CTAATTGACCTGTATATGCAA
* *
4201888 CTAA-TGACTTGTATTTGCA
1 CTAATTGACCTGTATATGCA
4201907 TTGCTTGTTT
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:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
CTAATTGACCTGTATATGCAA
Found at i:4202149 original size:17 final size:17
Alignment explanation
Indices: 4202127--4202159 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4202117 AAGATATAAA
4202127 GAAAGAGAA-AAAAGAAT
1 GAAAGA-AAGAAAAGAAT
4202144 GAAAGAAAGAAAAGAA
1 GAAAGAAAGAAAAGAA
4202160 CCTGCACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
GAAAGAAAGAAAAGAAT
Found at i:4202770 original size:61 final size:63
Alignment explanation
Indices: 4202639--4202773 Score: 193
Period size: 61 Copynumber: 2.2 Consensus size: 63
4202629 CCGTTGGAAA
* *
4202639 TTTCGTTGGAACATAAAACTTTAAAAAAAATTTTACAATCTTGTTGCAGTTTCCAATGAAAAT
1 TTTCGTTGGAACATAAAACTTTAAAAAAAATTTTACAATCTTGTTACAGTTTCCAACGAAAAT
* * * * *
4202702 TTCCGTTGGAACATTAAACTTTAAAAAAAA-TTTA-AATTTTTTTACAGTTTCCAACGAAATT
1 TTTCGTTGGAACATAAAACTTTAAAAAAAATTTTACAATCTTGTTACAGTTTCCAACGAAAAT
4202763 TTTCGTTGGAA
1 TTTCGTTGGAA
4202774 ATCTGTTGGA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
61 32 0.50
62 4 0.06
63 28 0.44
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (63 bp):
TTTCGTTGGAACATAAAACTTTAAAAAAAATTTTACAATCTTGTTACAGTTTCCAACGAAAAT
Found at i:4202960 original size:81 final size:81
Alignment explanation
Indices: 4202804--4202962 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 81
4202794 AGTCAATGAT
**
4202804 ATATTAAAAATGTAACTTTCCAATGGAATTTTCGTTGAAAAATTCTGTTGGAAAGAGCCTTTTTA
1 ATATTAAAAATGTAACTTTCCAACAGAATTTTCGTTGAAAAATTCTGTTGGAAAGAGCCTTTTTA
4202869 TTGCATCAAAGTGNAAC
66 TTGCATCAAAGTG-AAC
* *
4202886 ATATTAAAAATGTAACTTTCCAACAGAATTTTCGTTGGAAATTTC-GTTGGAAAGAGCCTTTTTA
1 ATATTAAAAATGTAACTTTCCAACAGAATTTTCGTTGAAAAATTCTGTTGGAAAGAGCCTTTTTA
4202950 TTGCATCAAAGTG
66 TTGCATCAAAGTG
4202963 TTACTGATGT
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 32 0.44
82 41 0.56
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (81 bp):
ATATTAAAAATGTAACTTTCCAACAGAATTTTCGTTGAAAAATTCTGTTGGAAAGAGCCTTTTTA
TTGCATCAAAGTGAAC
Found at i:4204608 original size:90 final size:89
Alignment explanation
Indices: 4204480--4204642 Score: 227
Period size: 90 Copynumber: 1.8 Consensus size: 89
4204470 CAGAAGGCGG
* * *
4204480 AAGCCCCAGCTCTCTCTACAACCGACGGCACAGGAACCCAAATCTGGTCGGCTCTCGCTTCTTCC
1 AAGCCCCAGCTCTCTCTACAACCGACGGCAAAGCAACCCAAATCTGGTC-GCTCTAGCTTCTTCC
4204545 TTTTCCAGCCGGTGACACAACCCCA
65 TTTTCCAGCCGGTGACACAACCCCA
* * * * * * *
4204570 AAGCCCCAGCTGTCTCTAGAACCGGCGGCAAAGCAACCCAGATCTTGTCTCTCTAGCTTCTTCTT
1 AAGCCCCAGCTCTCTCTACAACCGACGGCAAAGCAACCCAAATCTGGTCGCTCTAGCTTCTTCCT
4204635 TTTCCAGC
66 TTTCCAGC
4204643 AAGCGACACA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 21 0.33
90 42 0.67
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.23
Consensus pattern (89 bp):
AAGCCCCAGCTCTCTCTACAACCGACGGCAAAGCAACCCAAATCTGGTCGCTCTAGCTTCTTCCT
TTTCCAGCCGGTGACACAACCCCA
Found at i:4205640 original size:35 final size:35
Alignment explanation
Indices: 4205594--4205662 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
4205584 GGTTCTCCAT
*
4205594 ATATTTATTTTTTGTTATTT-AATTTTAAGTTTAAG
1 ATATTTATTTTTTATTATTTAAATTTTAA-TTTAAG
*
4205629 ATATTTGTTTTTTATTATTTAAATTTTAATTTAA
1 ATATTTATTTTTTATTATTTAAATTTTAATTTAA
4205663 ATTTTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 23 0.74
36 8 0.26
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (35 bp):
ATATTTATTTTTTATTATTTAAATTTTAATTTAAG
Found at i:4210307 original size:6 final size:6
Alignment explanation
Indices: 4210298--4210341 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
4210288 GGAGAAGATA
* *
4210298 ATGAAG ATGATG ATGAAG ATGAAG ATGAAG ATGAAG ATAAAG AT
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG AT
4210342 CATGTGGAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:4211729 original size:16 final size:16
Alignment explanation
Indices: 4211708--4211747 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
4211698 AGGATGGTAT
4211708 GAATTAATGTTACTCA
1 GAATTAATGTTACTCA
4211724 GAATTAATGTTACTCA
1 GAATTAATGTTACTCA
4211740 GAATTAAT
1 GAATTAAT
4211748 ATGTATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (16 bp):
GAATTAATGTTACTCA
Found at i:4219084 original size:17 final size:19
Alignment explanation
Indices: 4219052--4219089 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4219042 CATATGGTAA
4219052 TTAGATATACCCA-TTTCC
1 TTAGATATACCCATTTTCC
*
4219070 TTAGAT-TACCGATTTTCC
1 TTAGATATACCCATTTTCC
4219088 TT
1 TT
4219090 CCATTTCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.45
Consensus pattern (19 bp):
TTAGATATACCCATTTTCC
Found at i:4229556 original size:125 final size:125
Alignment explanation
Indices: 4229334--4229582 Score: 392
Period size: 125 Copynumber: 2.0 Consensus size: 125
4229324 AATAAATTGA
* *
4229334 AAAAGTGGAGGAATGGTGCAGTATCAGGCTACTAGACTTGGTAACAGGAACATCCCCTGATTTTA
1 AAAAGTGGAGGAATGGTGCAGTATCAGGCTACTAGACTTGGTAACAGCAACATCCCCTGATTGTA
* *
4229399 GTGTTGCAATTACTTTTTGGTTTGGGTTTAGGCCTTTGATA-GCTGGAATCAGAAGGAAAT
66 GTGTTGCAATTACTTTTTGGTTTGGCTTTAGGCCCTTGATACG-TGGAATCAGAAGGAAAT
* * * *
4229459 AAAAGTGGAGGAATGGTGCTGTATCAGGCTACTGGACTTGGTAACAGCAACATTCCTTGATTGTA
1 AAAAGTGGAGGAATGGTGCAGTATCAGGCTACTAGACTTGGTAACAGCAACATCCCCTGATTGTA
* *
4229524 GTGTTGCTATTACTTTTTGGTTTGGCTTTAGGCCCTTGATACGTGGAATCAGGAGGAAA
66 GTGTTGCAATTACTTTTTGGTTTGGCTTTAGGCCCTTGATACGTGGAATCAGAAGGAAA
4229583 CAGTGGGCCA
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
125 112 0.99
126 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.32
Consensus pattern (125 bp):
AAAAGTGGAGGAATGGTGCAGTATCAGGCTACTAGACTTGGTAACAGCAACATCCCCTGATTGTA
GTGTTGCAATTACTTTTTGGTTTGGCTTTAGGCCCTTGATACGTGGAATCAGAAGGAAAT
Found at i:4242662 original size:63 final size:64
Alignment explanation
Indices: 4242544--4242736 Score: 234
Period size: 63 Copynumber: 3.0 Consensus size: 64
4242534 TTAAAATAAA
* * * *
4242544 TATATTAAAAAAAATTGAATTTATTTCTTTTCAAAACAAT-AGGCTTAATACATGTATTGATTAA
1 TATATTAAAAAATATTGAATTTATTT-TTTTCAAAATATTGA-ACTTAATACATGTATTGATTAA
4242608 T
64 T
4242609 TA-ATTAACAAAATATTGAATTTATTTTTTTCAAAATATTGAACTT-ATACATGTATTGATTAAT
1 TATATTAA-AAAATATTGAATTTATTTTTTTCAAAATATTGAACTTAATACATGTATTGATTAAT
* * * * * *
4242672 TATTTTAAAAAGTATT--TTTTATTTTTGTGAAAATATTGAACTTAATGCATGTATTGATTAAT
1 TATATTAAAAAATATTGAATTTATTTTTTTCAAAATATTGAACTTAATACATGTATTGATTAAT
4242734 TAT
1 TAT
4242737 TTAGTCGATA
Statistics
Matches: 114, Mismatches: 10, Indels: 11
0.84 0.07 0.08
Matches are distributed among these distances:
61 24 0.21
62 20 0.18
63 27 0.24
64 23 0.20
65 20 0.18
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (64 bp):
TATATTAAAAAATATTGAATTTATTTTTTTCAAAATATTGAACTTAATACATGTATTGATTAAT
Found at i:4242809 original size:22 final size:22
Alignment explanation
Indices: 4242781--4242822 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4242771 ATCAATTAAT
*
4242781 AATTTA-TATATTAATCAAAACA
1 AATTTATTA-ATTAATAAAAACA
4242803 AATTTATTAATTAATAAAAA
1 AATTTATTAATTAATAAAAA
4242823 ATTAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTATTAATTAATAAAAACA
Found at i:4250395 original size:126 final size:126
Alignment explanation
Indices: 4250167--4250395 Score: 264
Period size: 126 Copynumber: 1.8 Consensus size: 126
4250157 TATATTTTAG
* * *
4250167 TTGTAAATGTAAATCTATGATAAGTGGTATCAAAGCCTAGTCAAATCTTCATTAATATAAGACTC
1 TTGTAAATGTAAATATATGACAAATGGTATCAAAGCCTAGTCAAATCTTCATTAATATAAGACTC
** * *
4250232 TTTCATGAAATATTTTAGAGTTGAAATAAATGATATCAGAACTTACAAACATGTTTTTCAA
66 TTTCATGAAATATACTAGAGTAGAAACAAATGATATCAGAACTTACAAACATGTTTTTCAA
* * * * *
4250293 TTGTAAATGTAGATATATGACAAATGGTATCAGAGTCTA-TCCAAA-CTTTTATTAATATAATAC
1 TTGTAAATGTAAATATATGACAAATGGTATCAAAGCCTAGT-CAAATC-TTCATTAATATAAGAC
* * * * * *
4250356 TTTTTTATGAAATATACTATAGTAGAGACAAGTGGTATCA
64 TCTTTCATGAAATATACTAGAGTAGAAACAAATGATATCA
4250396 TAACCTACCA
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
125 2 0.02
126 81 0.98
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (126 bp):
TTGTAAATGTAAATATATGACAAATGGTATCAAAGCCTAGTCAAATCTTCATTAATATAAGACTC
TTTCATGAAATATACTAGAGTAGAAACAAATGATATCAGAACTTACAAACATGTTTTTCAA
Found at i:4252781 original size:2 final size:2
Alignment explanation
Indices: 4252770--4252813 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4252760 ACCTTAGTAT
*
4252770 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4252811 TA T
1 TA T
4252814 TATTTCTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4264949 original size:20 final size:20
Alignment explanation
Indices: 4264924--4264964 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4264914 GAAAATTAAG
4264924 TATGCTTTTTCTTTCATTTA
1 TATGCTTTTTCTTTCATTTA
4264944 TATGCTTTTTCTTTCATTTA
1 TATGCTTTTTCTTTCATTTA
4264964 T
1 T
4264965 GATCAACTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TATGCTTTTTCTTTCATTTA
Found at i:4269649 original size:293 final size:293
Alignment explanation
Indices: 4269122--4269705 Score: 1159
Period size: 293 Copynumber: 2.0 Consensus size: 293
4269112 TGTGAGGGAC
4269122 AGAGGGCATGCATCACCTTTCCACTATATTTCCCTTTCCAATAGTTTTGTTTCAATCAGATCTTT
1 AGAGGGCATGCATCACCTTTCCACTATATTTCCCTTTCCAATAGTTTTGTTTCAATCAGATCTTT
4269187 GAAATGGTCAACAGAAATGTTCTAGTTAATGTCACCCTGTAACTACATTTGTGGACTTGGGGTCA
66 GAAATGGTCAACAGAAATGTTCTAGTTAATGTCACCCTGTAACTACATTTGTGGACTTGGGGTCA
4269252 ATGATTTTAGCTTTCATTGAGAAGAATTGAATGGTAATTCAAAGTCTTTGAAAATTAGAAATTGA
131 ATGATTTTAGCTTTCATTGAGAAGAATTGAATGGTAATTCAAAGTCTTTGAAAATTAGAAATTGA
4269317 AATAAACTATGATTATTGTTTATTTACCTTCTTAAAAAAATTTGATGCAGGTTGTTGAACAGGAC
196 AATAAACTATGATTATTGTTTATTTACCTTCTTAAAAAAATTTGATGCAGGTTGTTGAACAGGAC
4269382 ACTTTCATACAACAAATTTCTCTTTATATATAT
261 ACTTTCATACAACAAATTTCTCTTTATATATAT
*
4269415 AGAGGGCATGCATCACCTTTCCACTATATTTCCCTTTCCAATAGTTTTGTTTCAATTAGATCTTT
1 AGAGGGCATGCATCACCTTTCCACTATATTTCCCTTTCCAATAGTTTTGTTTCAATCAGATCTTT
4269480 GAAATGGTCAACAGAAATGTTCTAGTTAATGTCACCCTGTAACTACATTTGTGGACTTGGGGTCA
66 GAAATGGTCAACAGAAATGTTCTAGTTAATGTCACCCTGTAACTACATTTGTGGACTTGGGGTCA
4269545 ATGATTTTAGCTTTCATTGAGAAGAATTGAATGGTAATTCAAAGTCTTTGAAAATTAGAAATTGA
131 ATGATTTTAGCTTTCATTGAGAAGAATTGAATGGTAATTCAAAGTCTTTGAAAATTAGAAATTGA
4269610 AATAAACTATGATTATTGTTTATTTACCTTCTTAAAAAAATTTGATGCAGGTTGTTGAACAGGAC
196 AATAAACTATGATTATTGTTTATTTACCTTCTTAAAAAAATTTGATGCAGGTTGTTGAACAGGAC
4269675 ACTTTCATACAACAAATTTCTCTTTATATAT
261 ACTTTCATACAACAAATTTCTCTTTATATAT
4269706 TATAATATAT
Statistics
Matches: 290, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
293 290 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (293 bp):
AGAGGGCATGCATCACCTTTCCACTATATTTCCCTTTCCAATAGTTTTGTTTCAATCAGATCTTT
GAAATGGTCAACAGAAATGTTCTAGTTAATGTCACCCTGTAACTACATTTGTGGACTTGGGGTCA
ATGATTTTAGCTTTCATTGAGAAGAATTGAATGGTAATTCAAAGTCTTTGAAAATTAGAAATTGA
AATAAACTATGATTATTGTTTATTTACCTTCTTAAAAAAATTTGATGCAGGTTGTTGAACAGGAC
ACTTTCATACAACAAATTTCTCTTTATATATAT
Found at i:4269715 original size:2 final size:2
Alignment explanation
Indices: 4269699--4269781 Score: 104
Period size: 2 Copynumber: 43.5 Consensus size: 2
4269689 AATTTCTCTT
*
4269699 TA TA TA T- TA TA -A TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4269739 TA TA TA TA TA -A TA TA T- TA CTT TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
4269779 TA T
1 TA T
4269782 TCAATGGTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
1 5 0.07
2 65 0.92
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4275007 original size:2 final size:2
Alignment explanation
Indices: 4274952--4274987 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4274942 TTGTTGATAA
*
4274952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4274988 GTGCGTGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4275505 original size:2 final size:2
Alignment explanation
Indices: 4275493--4275529 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4275483 GAGATTGATA
*
4275493 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4275530 CTTGCAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4279158 original size:24 final size:24
Alignment explanation
Indices: 4279129--4279178 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
4279119 AGAGAATAAG
*
4279129 AATTTGAACCCTACTCTTTAGATA
1 AATTTGAACCCTACTCTTTAAATA
***
4279153 AATTTGAATGTTACTCTTTAAATA
1 AATTTGAACCCTACTCTTTAAATA
4279177 AA
1 AA
4279179 AGATCATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (24 bp):
AATTTGAACCCTACTCTTTAAATA
Found at i:4291688 original size:4 final size:4
Alignment explanation
Indices: 4291664--4291713 Score: 59
Period size: 4 Copynumber: 12.2 Consensus size: 4
4291654 GTGTAGACAC
4291664 ATAA ATAA A-AA A-AA ATAAA ATAA ATAA ATAA ATTAA ATAA ATTAA ATAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA A-TAA ATAA A-TAA ATAA
4291713 A
1 A
4291714 AAAAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.14
4 24 0.57
5 12 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:4291688 original size:9 final size:9
Alignment explanation
Indices: 4291664--4291726 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
4291654 GTGTAGACAC
4291664 ATAAATAAAA
1 ATAAAT-AAA
*
4291674 AAAAATAAA
1 ATAAATAAA
4291683 ATAAAT-AA
1 ATAAATAAA
*
4291691 ATAAATTAA
1 ATAAATAAA
*
4291700 ATAAATTAA
1 ATAAATAAA
*
4291709 ATAAAAAAA
1 ATAAATAAA
4291718 ATAAA-AAA
1 ATAAATAAA
4291726 A
1 A
4291727 AATCGGGATG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
8 12 0.25
9 31 0.65
10 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAATAAA
Found at i:4291727 original size:13 final size:13
Alignment explanation
Indices: 4291664--4291728 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
4291654 GTGTAGACAC
4291664 ATAAATAAAAAAAA
1 ATAAA-AAAAAAAA
* *
4291678 ATAAAATAAATAA
1 ATAAAAAAAAAAA
* *
4291691 ATAAATTAAATAAA
1 ATAAA-AAAAAAAA
* *
4291705 TTAAATAAAAAAA
1 ATAAAAAAAAAAA
4291718 ATAAAAAAAAA
1 ATAAAAAAAAA
4291729 TCGGGATGGC
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
13 27 0.68
14 13 0.32
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAAAAAAAAAA
Found at i:4297104 original size:21 final size:21
Alignment explanation
Indices: 4297078--4297120 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4297068 CATTTGGTGT
4297078 CAATATGTGAAATATATCCTA
1 CAATATGTGAAATATATCCTA
4297099 CAATATGTGAAATATATCCTA
1 CAATATGTGAAATATATCCTA
4297120 C
1 C
4297121 TGGTTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (21 bp):
CAATATGTGAAATATATCCTA
Found at i:4305443 original size:20 final size:21
Alignment explanation
Indices: 4305403--4305443 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4305393 AATTTTTTGT
4305403 AAATTTTTATGAATCGAATTTA
1 AAATTTTTA-GAATCGAATTTA
*
4305425 AAATTTTTA-AATTGAATTT
1 AAATTTTTAGAATCGAATTT
4305444 TGAGTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
AAATTTTTAGAATCGAATTTA
Found at i:4307473 original size:2 final size:2
Alignment explanation
Indices: 4307466--4307499 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4307456 TATTTAATTA
4307466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4307500 TTGTGCCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4318898 original size:36 final size:37
Alignment explanation
Indices: 4318850--4318922 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
4318840 TCAATCGGGC
*
4318850 TGACAATGAATAATGA-ATAAC-TTTTTCATACATTAA
1 TGACAATAAATAAT-ATATAACTTTTTTCATACATTAA
*
4318886 TGACAATAAATAATATGTAACTTTTTTCATACATTAA
1 TGACAATAAATAATATATAACTTTTTTCATACATTAA
4318923 GAATGTATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 1 0.03
36 17 0.52
37 15 0.45
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (37 bp):
TGACAATAAATAATATATAACTTTTTTCATACATTAA
Found at i:4320312 original size:120 final size:118
Alignment explanation
Indices: 4320103--4320405 Score: 366
Period size: 120 Copynumber: 2.6 Consensus size: 118
4320093 AAATAGTGTA
* * *
4320103 ACTAATTCTTCTATGTTTG-T--TTTTTTTATCGAACATTATACAGTTTAAGATTC-GATTTTTA
1 ACTAATTCTTCTATTTTTGTTGATTTTTTTATCGAAAACTATACA-TTTAAGATTCAG-TTTTTA
* * * ** * *
4320164 TATGTACGATAACGTACTTTTCATTACAACACCATCTATTTTGATCCTT-TACGCT
64 AATGTACAATAACATACTTACCATTACAACACCAACTATTTTGAT-CTTATACACT
*
4320219 ACTAATTCTTCTATTTTTGTTGATTTTTTTATCGAAAACTATACAATTTTAAAATTCAGTTTTTA
1 ACTAATTCTTCTATTTTTGTTGATTTTTTTATCGAAAACTATAC-A-TTTAAGATTCAGTTTTTA
* *
4320284 AATGTACAATGATATACTTACCATTACAACACCAACTATTTTGATCTTATACACT
64 AATGTACAATAACATACTTACCATTACAACACCAACTATTTTGATCTTATACACT
* * *
4320339 ACTAATTCTTCTATTCTTGTTGA-TTTTTTATCGAAAACTATATGATTTAAGATTCAATTTTTAA
1 ACTAATTCTTCTATTTTTGTTGATTTTTTTATCGAAAACTATA-CATTTAAGATTCAGTTTTTAA
4320403 ATG
65 ATG
4320406 CATGATAATA
Statistics
Matches: 162, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
116 18 0.11
117 1 0.01
118 20 0.12
119 42 0.26
120 80 0.49
121 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (118 bp):
ACTAATTCTTCTATTTTTGTTGATTTTTTTATCGAAAACTATACATTTAAGATTCAGTTTTTAAA
TGTACAATAACATACTTACCATTACAACACCAACTATTTTGATCTTATACACT
Found at i:4345706 original size:6 final size:6
Alignment explanation
Indices: 4345697--4345723 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4345687 TATATTTCAA
4345697 TTTCCT TTTCCT TTTCCT TTTCCT TTT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTT
4345724 GATTTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCCT
Found at i:4360398 original size:14 final size:15
Alignment explanation
Indices: 4360351--4360398 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
4360341 ATGACTCCCA
4360351 ATCTC-CCA-TCTCC
1 ATCTCTCCACTCTCC
*
4360364 AGCTCTCCACTCTCC
1 ATCTCTCCACTCTCC
*
4360379 AT-TCTCCACT-TTC
1 ATCTCTCCACTCTCC
4360392 ATCTCTC
1 ATCTCTC
4360399 GCCCTTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 8 0.28
14 15 0.52
15 6 0.21
ACGTcount: A:0.15, C:0.48, G:0.02, T:0.35
Consensus pattern (15 bp):
ATCTCTCCACTCTCC
Found at i:4377304 original size:22 final size:25
Alignment explanation
Indices: 4377278--4377333 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
4377268 AAGTCTAGAC
4377278 TTATTTATTT-TAA-TATTA-AATT
1 TTATTTATTTATAACTATTATAATT
4377300 TTATTATATTTGATAACTATTATAATT
1 TTATT-TATTT-ATAACTATTATAATT
4377327 TT-TTTAT
1 TTATTTAT
4377334 GAATTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
25 6 0.21
26 7 0.24
27 6 0.21
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATTTATTTATAACTATTATAATT
Found at i:4378060 original size:63 final size:63
Alignment explanation
Indices: 4377993--4378113 Score: 192
Period size: 63 Copynumber: 1.9 Consensus size: 63
4377983 ATAATATATG
*
4377993 CAAATTGAATTCC-AATCTTAATTATATAATCT-AATCTAAAAGTTTAAATCAGATTACAACATT
1 CAAATTGAA-TCCTAATCTTAATTATATAAT-TAAATATAAAAGTTTAAATCAGATTACAACATT
*
4378056 CAAATTGAATCCTAATCTTAATTATATAATTAAATATAAAGGTTTAAATCAGATTACA
1 CAAATTGAATCCTAATCTTAATTATATAATTAAATATAAAAGTTTAAATCAGATTACA
4378114 TCCCAAGACC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
62 4 0.07
63 50 0.93
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (63 bp):
CAAATTGAATCCTAATCTTAATTATATAATTAAATATAAAAGTTTAAATCAGATTACAACATT
Found at i:4379778 original size:66 final size:66
Alignment explanation
Indices: 4379672--4380004 Score: 477
Period size: 66 Copynumber: 5.0 Consensus size: 66
4379662 ATCTTCTTCA
* * * * *
4379672 TCATCGCTTGATTCGTCAGTTATTTCATTACCAGCATTACTCTCACTCCAAGCATCAATTACTTG
1 TCATCACTTGAATCGTCAGTTGTTTCATCACTAGCATTACTCTCACTCCAAGCATCAATTACTTG
4379737 G
66 G
* * * * *
4379738 TCATCACTTGAATCGTCAGTTGTTTCATCACTGGCATTACTCTCACTCCCAGCGTCAATTTCCTG
1 TCATCACTTGAATCGTCAGTTGTTTCATCACTAGCATTACTCTCACTCCAAGCATCAATTACTTG
4379803 G
66 G
* * *
4379804 TCATGACTTGAATAGTCAGTTGCTTCATCACTAGCATTACTCTCACTCCAAGCATCAATTACTTG
1 TCATCACTTGAATCGTCAGTTGTTTCATCACTAGCATTACTCTCACTCCAAGCATCAATTACTTG
4379869 G
66 G
* * *
4379870 TCATCACTTGAATCTTCAGTTGTTTCATCACTAGCATTACTCTCACTTCAAGCATCAATTACTTC
1 TCATCACTTGAATCGTCAGTTGTTTCATCACTAGCATTACTCTCACTCCAAGCATCAATTACTTG
4379935 G
66 G
* * * * *
4379936 TCATCACTTGAATAGTCAGTTGCTTCATCACTAGCATCACTCTCACTCCTAGCATCAGTTACTTG
1 TCATCACTTGAATCGTCAGTTGTTTCATCACTAGCATTACTCTCACTCCAAGCATCAATTACTTG
4380001 G
66 G
4380002 TCA
1 TCA
4380005 AGTAATACTA
Statistics
Matches: 235, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 235 1.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (66 bp):
TCATCACTTGAATCGTCAGTTGTTTCATCACTAGCATTACTCTCACTCCAAGCATCAATTACTTG
G
Found at i:4381186 original size:48 final size:48
Alignment explanation
Indices: 4381130--4381230 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 48
4381120 GCATGGAACG
* *
4381130 ATCCCTTGTTTTGACATATTTTCTGGGTAGATTCCGTAACACCCTCTT
1 ATCCCTTGTTCTGACATACTTTCTGGGTAGATTCCGTAACACCCTCTT
* * *
4381178 ATCCCTTGTTCTGACATCCTTTCTGGGTAGATTCTGTAACATCCTCTT
1 ATCCCTTGTTCTGACATACTTTCTGGGTAGATTCCGTAACACCCTCTT
4381226 A-CCCT
1 ATCCCT
4381231 CCTATATTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 4 0.08
48 44 0.92
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.41
Consensus pattern (48 bp):
ATCCCTTGTTCTGACATACTTTCTGGGTAGATTCCGTAACACCCTCTT
Found at i:4382672 original size:12 final size:12
Alignment explanation
Indices: 4382646--4382858 Score: 59
Period size: 13 Copynumber: 17.0 Consensus size: 12
4382636 TATTATTTTT
*
4382646 TAAAAAATTAAAA
1 TAAAAAA-TATAA
*
4382659 TAAAATATATAATA
1 TAAAAAATAT-A-A
*
4382673 TAAAAAATTATAT
1 TAAAAAA-TATAA
*
4382686 TAAAAAATAAAA
1 TAAAAAATATAA
4382698 T-AAAAATAT-A
1 TAAAAAATATAA
*
4382708 T-AAAATTATAA
1 TAAAAAATATAA
*
4382719 T-AAAAATAAAA
1 TAAAAAATATAA
* *
4382730 TATATAATAT--
1 TAAAAAATATAA
*
4382740 TAAAATTATATTAA
1 TAAAA-AATA-TAA
4382754 -AAAGATAATATTACA
1 TAAA-A-AATA-TA-A
*
4382769 TAAAAATTGATAA
1 TAAAAAAT-ATAA
4382782 TAAAAAATATAAA
1 TAAAAAATAT-AA
* *
4382795 TATATAATAT--
1 TAAAAAATATAA
*
4382805 TAAAATTATATTAA
1 TAAAA-AATA-TAA
4382819 -AAAGATAATATTATA
1 TAAA-A-AATA-TA-A
*
4382834 TAAAAATTGATAA
1 TAAAAAAT-ATAA
4382847 TAAAAAATATAA
1 TAAAAAATATAA
4382859 ATATATTAAA
Statistics
Matches: 151, Mismatches: 27, Indels: 45
0.68 0.12 0.20
Matches are distributed among these distances:
10 15 0.10
11 24 0.16
12 19 0.13
13 46 0.30
14 32 0.21
15 9 0.06
16 6 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
TAAAAAATATAA
Found at i:4382676 original size:27 final size:25
Alignment explanation
Indices: 4382646--4382713 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
4382636 TATTATTTTT
*
4382646 TAAAAAATTAAAATAAAATATATAATA
1 TAAAAAATTAAAATAAAA-A-ATAAAA
* *
4382673 TAAAAAATTATATTAAAAAATAAAA
1 TAAAAAATTAAAATAAAAAATAAAA
4382698 TAAAAATATATAAAAT
1 TAAAAA-AT-TAAAAT
4382714 TATAATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 11 0.32
26 3 0.09
27 20 0.59
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAAAATTAAAATAAAAAATAAAA
Found at i:4382680 original size:21 final size:21
Alignment explanation
Indices: 4382655--4382744 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 21
4382645 TTAAAAAATT
*
4382655 AAAATAAAATATATAATATAA
1 AAAATAAAATATAAAATATAA
* * *
4382676 AAAATTATAT-TAAAAAATAA
1 AAAATAAAATATAAAATATAA
4382696 AATAA-AAATATATAAAATTATAATA
1 AA-AATAAA-ATATAAAA-TAT-A-A
* *
4382721 AAAATAAAATATATAATATTA
1 AAAATAAAATATAAAATATAA
4382742 AAA
1 AAA
4382745 TTATATTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
20 11 0.21
21 16 0.30
22 5 0.09
23 5 0.09
24 10 0.19
25 6 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATAAAATATAAAATATAA
Found at i:4382688 original size:32 final size:31
Alignment explanation
Indices: 4382652--4382889 Score: 163
Period size: 32 Copynumber: 7.5 Consensus size: 31
4382642 TTTTTAAAAA
*
4382652 ATTAAAATAAAATATATAATATAAAAAATTAT
1 ATTAAAATAAAATATATAATAT-TAAAATTAT
*
4382684 ATTAAAAAATAAAATA-AAAATATATAAAATTAT
1 ATT--AAAATAAAATATATAATAT-TAAAATTAT
*
4382717 AATAAAAATAAAATATATAATATTAAAATTAT
1 -ATTAAAATAAAATATATAATATTAAAATTAT
4382749 ATTAAAA-AGATAATAT-TACATA--AAAATTGAT
1 ATTAAAATA-A-AATATATA-ATATTAAAATT-AT
*
4382780 AATAAAAAATATAAATATATAATATTAAAATTAT
1 -AT-TAAAATA-AAATATATAATATTAAAATTAT
*
4382814 ATTAAAA-AGATAATAT-T-ATATAAAAATTGAT
1 ATTAAAATA-A-AATATATAATATTAAAATT-AT
* * * * *
4382845 AATAAAA-AATATAAAT-ATATTAAACTTAC
1 ATTAAAATAAAATATATAATATTAAAATTAT
**
4382874 ATTTTAATAAAATATA
1 ATTAAAATAAAATATA
4382890 ATTTTAAAAA
Statistics
Matches: 167, Mismatches: 21, Indels: 38
0.74 0.09 0.17
Matches are distributed among these distances:
29 8 0.05
30 34 0.20
31 23 0.14
32 42 0.25
33 35 0.21
34 19 0.11
35 6 0.04
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (31 bp):
ATTAAAATAAAATATATAATATTAAAATTAT
Found at i:4382702 original size:11 final size:11
Alignment explanation
Indices: 4382688--4382731 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
4382678 AATTATATTA
4382688 AAAAATAAAAT
1 AAAAATAAAAT
*
4382699 AAAAAT-ATAT
1 AAAAATAAAAT
* *
4382709 AAAATTATAAT
1 AAAAATAAAAT
4382720 AAAAATAAAAT
1 AAAAATAAAAT
4382731 A
1 A
4382732 TATAATATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:4382713 original size:33 final size:34
Alignment explanation
Indices: 4382655--4382864 Score: 214
Period size: 33 Copynumber: 6.4 Consensus size: 34
4382645 TTAAAAAATT
*
4382655 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAATATATAATATATAAAATTATATTAA
* *
4382689 AAAATAAAATA-AAAATATATAAAATTATAAT-A
1 AAAATAAAATATATAATATATAAAATTATATTAA
4382721 AAAATAAAATATATAATAT-TAAAATTATATTAA
1 AAAATAAAATATATAATATATAAAATTATATTAA
* *
4382754 AAAGAT--AATAT-T-ACATA-AAAATTGATAATAA
1 AAA-ATAAAATATATAATATATAAAATT-ATATTAA
4382785 AAAATATAAATATATAATAT-TAAAATTATATTAA
1 AAAATA-AAATATATAATATATAAAATTATATTAA
*
4382819 AAAGAT--AATAT-T-ATATA-AAAATTGATAATAA
1 AAA-ATAAAATATATAATATATAAAATT-ATATTAA
4382850 AAAATATAAATATAT
1 AAAATA-AAATATAT
4382865 TAAACTTACA
Statistics
Matches: 148, Mismatches: 10, Indels: 36
0.76 0.05 0.19
Matches are distributed among these distances:
30 23 0.16
31 20 0.14
32 33 0.22
33 37 0.25
34 24 0.16
35 11 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (34 bp):
AAAATAAAATATATAATATATAAAATTATATTAA
Found at i:4382720 original size:26 final size:25
Alignment explanation
Indices: 4382658--4382741 Score: 84
Period size: 26 Copynumber: 3.4 Consensus size: 25
4382648 AAAAATTAAA
* *
4382658 ATAAAATATATAATATAAAAAATTAT
1 ATAAAAT-TATAATAAAAAAAAATAT
*
4382684 ATTAAA--A-AATAAAATAAAAATAT
1 ATAAAATTATAATAAAA-AAAAATAT
4382707 ATAAAATTATAATAAAAATAAAATAT
1 ATAAAATTATAATAAAAA-AAAATAT
*
4382733 ATAATATTA
1 ATAAAATTA
4382742 AAATTATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
22 6 0.12
23 13 0.27
25 2 0.04
26 27 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAAAATTATAATAAAAAAAAATAT
Found at i:4382750 original size:11 final size:11
Alignment explanation
Indices: 4382676--4382820 Score: 52
Period size: 11 Copynumber: 13.4 Consensus size: 11
4382666 TATAATATAA
4382676 AAAATTATATT
1 AAAATTATATT
* * *
4382687 AAAAAATAAAAT
1 -AAAATTATATT
*
4382699 AAAAATATA-T
1 AAAATTATATT
*
4382709 AAAATTATAAT
1 AAAATTATATT
* * *
4382720 AAAAATAAAAT
1 AAAATTATATT
* *
4382731 -ATATAATATT
1 AAAATTATATT
4382741 AAAATTATATT
1 AAAATTATATT
*
4382752 AAAA--AGA-T
1 AAAATTATATT
* * *
4382760 AATATTACATA
1 AAAATTATATT
*
4382771 AAAATTGATAAT
1 AAAATT-ATATT
*
4382783 AAAA-AATA-T
1 AAAATTATATT
4382792 AAATATATAATATT
1 AAA-AT-T-ATATT
4382806 AAAATTATATT
1 AAAATTATATT
4382817 AAAA
1 AAAA
4382821 AGATAATATT
Statistics
Matches: 98, Mismatches: 24, Indels: 23
0.68 0.17 0.16
Matches are distributed among these distances:
8 4 0.04
9 6 0.06
10 20 0.20
11 44 0.45
12 15 0.15
13 5 0.05
14 4 0.04
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (11 bp):
AAAATTATATT
Found at i:4382754 original size:26 final size:26
Alignment explanation
Indices: 4382682--4382775 Score: 84
Period size: 26 Copynumber: 3.6 Consensus size: 26
4382672 ATAAAAAATT
*
4382682 ATATTAAAAAATAAAATAAAAATATATA
1 ATATTAAAATA-AAAAT-AAAATATATA
* *
4382710 AAATTATAATAAAAATAAAATATATA
1 ATATTAAAATAAAAATAAAATATATA
* * * *
4382736 ATATTAAAATTATATTAAAA-AGATA
1 ATATTAAAATAAAAATAAAATATATA
*
4382761 ATATT-ACATAAAAAT
1 ATATTAAAATAAAAAT
4382776 TGATAATAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
24 6 0.11
25 9 0.17
26 25 0.47
27 5 0.09
28 8 0.15
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (26 bp):
ATATTAAAATAAAAATAAAATATATA
Found at i:4382795 original size:20 final size:20
Alignment explanation
Indices: 4382772--4382860 Score: 63
Period size: 20 Copynumber: 4.2 Consensus size: 20
4382762 TATTACATAA
4382772 AAATTGATAATAAAAAATAT
1 AAATTGATAATAAAAAATAT
4382792 AAATAT-ATAATATTAAAATTATATT
1 AAAT-TGATAATA--AAAA--ATA-T
** ** * *
4382817 AAAAAGATAATATTATATAA
1 AAATTGATAATAAAAAATAT
4382837 AAATTGATAATAAAAAATAT
1 AAATTGATAATAAAAAATAT
4382857 AAAT
1 AAAT
4382861 ATATTAAACT
Statistics
Matches: 50, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
20 28 0.56
21 4 0.08
22 4 0.08
23 1 0.02
24 3 0.06
25 10 0.20
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAATTGATAATAAAAAATAT
Found at i:4382810 original size:97 final size:94
Alignment explanation
Indices: 4382675--4382852 Score: 234
Period size: 97 Copynumber: 1.9 Consensus size: 94
4382665 ATATAATATA
* *
4382675 AAAAATTATATTAAAAAATAAAATAAAAATATATAAAATTATAATAAAAATAAAATATATAATAT
1 AAAAATTATAATAAAAAATAAAATAAAAATATATAAAATTATAATAAAAAGAAAATAT-T-ATAT
* *
4382740 TAAAATT-ATATTAAAAAGATAATATTACAT
64 AAAAATTGATAATAAAAAGATAATATTACAT
* * *
4382770 AAAAATTGATAATAAAAAATATAAATATATAATAT-TAAAATTATATTAAAAAGATAATATTATA
1 AAAAATT-ATAATAAAAAATA-AAATA-AAAATATATAAAATTATAATAAAAAGAAAATATTATA
4382834 TAAAAATTGATAATAAAAA
63 TAAAAATTGATAATAAAAA
4382853 ATATAAATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
95 17 0.24
96 22 0.31
97 27 0.38
98 6 0.08
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (94 bp):
AAAAATTATAATAAAAAATAAAATAAAAATATATAAAATTATAATAAAAAGAAAATATTATATAA
AAATTGATAATAAAAAGATAATATTACAT
Found at i:4382885 original size:65 final size:65
Alignment explanation
Indices: 4382655--4382864 Score: 304
Period size: 65 Copynumber: 3.2 Consensus size: 65
4382645 TTAAAAAATT
* **
4382655 AAAATA-AAATATATAATATAAAAAATTATATTAAAAA-ATAAAATAAAAATATATAAAATT-AT
1 AAAATATAAATATATAATAT-TAAAATTATATTAAAAAGAT--AAT-ATTATATA-AAAATTGAT
4382717 AAT-A
61 AATAA
*
4382721 AAAATA-AAATATATAATATTAAAATTATATTAAAAAGATAATATTACATAAAAATTGATAATAA
1 AAAATATAAATATATAATATTAAAATTATATTAAAAAGATAATATTATATAAAAATTGATAATAA
4382785 AAAATATAAATATATAATATTAAAATTATATTAAAAAGATAATATTATATAAAAATTGATAATAA
1 AAAATATAAATATATAATATTAAAATTATATTAAAAAGATAATATTATATAAAAATTGATAATAA
4382850 AAAATATAAATATAT
1 AAAATATAAATATAT
4382865 TAAACTTACA
Statistics
Matches: 135, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
62 6 0.04
63 10 0.07
64 10 0.07
65 88 0.65
66 21 0.16
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (65 bp):
AAAATATAAATATATAATATTAAAATTATATTAAAAAGATAATATTATATAAAAATTGATAATAA
Found at i:4384295 original size:13 final size:13
Alignment explanation
Indices: 4384277--4384302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4384267 GTATGTTTAG
4384277 TGTGATTTGCTTT
1 TGTGATTTGCTTT
4384290 TGTGATTTGCTTT
1 TGTGATTTGCTTT
4384303 AGAATCTTTA
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:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (13 bp):
TGTGATTTGCTTT
Found at i:4385351 original size:25 final size:25
Alignment explanation
Indices: 4385317--4385367 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
4385307 CTATGGTCAT
* *
4385317 GCTCGGGAAATCATTTTTATATCCA
1 GCTCAGGAAATAATTTTTATATCCA
4385342 GCTCAGGAAATAATTTTTATATCCA
1 GCTCAGGAAATAATTTTTATATCCA
4385367 G
1 G
4385368 TGTCAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (25 bp):
GCTCAGGAAATAATTTTTATATCCA
Found at i:4395779 original size:67 final size:67
Alignment explanation
Indices: 4395671--4395806 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 67
4395661 AAGATCGGTT
*
4395671 TTCCGATTCCACAAAGATTTTCGAATTTAAACTCATAACTTCAACATACACATGAGCATTTGACT
1 TTCCGATTCCACAAAGATTTTCGAATTTAAACTCATAACTTCAACATACACACGAGCATTTGACT
4395736 CA
66 CA
* * *
4395738 TTCCGGTTCTACAAAGATTTTCGAATTTAAACTCATAACTTCAACATACATACGAGCATTTGACT
1 TTCCGATTCCACAAAGATTTTCGAATTTAAACTCATAACTTCAACATACACACGAGCATTTGACT
4395803 CA
66 CA
4395805 TT
1 TT
4395807 GATTCATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (67 bp):
TTCCGATTCCACAAAGATTTTCGAATTTAAACTCATAACTTCAACATACACACGAGCATTTGACT
CA
Found at i:4395870 original size:2 final size:2
Alignment explanation
Indices: 4395863--4395954 Score: 157
Period size: 2 Copynumber: 45.5 Consensus size: 2
4395853 CCATTCCTTC
4395863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
4395905 ANC CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4395948 AT AT AT A
1 AT AT AT A
4395955 ACCTTATGAC
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4406256 original size:2 final size:2
Alignment explanation
Indices: 4406251--4406290 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4406241 ACNNNNNNNN
4406251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4406291 TTGAATAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4409161 original size:23 final size:23
Alignment explanation
Indices: 4409135--4409184 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4409125 TATATTAATT
4409135 CTATATTAGAAAATTCAAATCTA
1 CTATATTAGAAAATTCAAATCTA
4409158 CTATATTAGAAAATTCAAATCTA
1 CTATATTAGAAAATTCAAATCTA
4409181 CTAT
1 CTAT
4409185 CCCTAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (23 bp):
CTATATTAGAAAATTCAAATCTA
Found at i:4410674 original size:29 final size:31
Alignment explanation
Indices: 4410641--4410719 Score: 101
Period size: 29 Copynumber: 2.6 Consensus size: 31
4410631 TATTCATGAA
4410641 AATTTAAATAAATTTTTATATTTTTA-TT-G
1 AATTTAAATAAATTTTTATATTTTTAGTTCG
* *
4410670 AATTTAATTAATTTTTTATATTTTTAGTTCG
1 AATTTAAATAAATTTTTATATTTTTAGTTCG
* *
4410701 -AGTCAAATAAATTTTTATA
1 AATTTAAATAAATTTTTATA
4410720 ATTAATTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.57
30 17 0.40
31 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (31 bp):
AATTTAAATAAATTTTTATATTTTTAGTTCG
Done.