Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 128 of 297
Found at i:44426670 original size:11 final size:11
Alignment explanation
Indices: 44426626--44426693 Score: 77
Period size: 11 Copynumber: 6.0 Consensus size: 11
44426616 AATAATATTT
44426626 AATATTTAAAA
1 AATATTTAAAA
*
44426637 AATAATGTT-TAA
1 AAT-AT-TTAAAA
44426649 AAT-TTTAAAAA
1 AATATTT-AAAA
44426660 AATATTTAAAA
1 AATATTTAAAA
44426671 AATATTTAAAAA
1 AATATTT-AAAA
44426683 AATATTTAAAA
1 AATATTTAAAA
44426694 TTTATAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
9 2 0.04
10 1 0.02
11 23 0.47
12 21 0.43
13 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:44426712 original size:11 final size:11
Alignment explanation
Indices: 44426629--44426716 Score: 53
Period size: 11 Copynumber: 8.0 Consensus size: 11
44426619 AATATTTAAT
44426629 ATTTAAAAAATA
1 ATTT-AAAAATA
*
44426641 ATGTTTAAAAT-
1 AT-TTAAAAATA
*
44426652 -TTTAAAAAAA
1 ATTTAAAAATA
44426662 TATTTAAAAA-A
1 -ATTTAAAAATA
44426673 TATTTAAAAA-A
1 -ATTTAAAAATA
*
44426684 ATATTTAAAAT-
1 AT-TTAAAAATA
44426695 -TTATAAAAATA
1 ATT-TAAAAATA
44426706 ATTTAAAAATA
1 ATTTAAAAATA
44426717 TATATTTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
9 7 0.11
10 10 0.16
11 26 0.42
12 17 0.27
13 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
ATTTAAAAATA
Found at i:44426725 original size:14 final size:12
Alignment explanation
Indices: 44426629--44426727 Score: 58
Period size: 12 Copynumber: 8.7 Consensus size: 12
44426619 AATATTTAAT
44426629 ATTTAAAAAATA
1 ATTTAAAAAATA
*
44426641 ATGTT-TAAAAT-
1 AT-TTAAAAAATA
44426652 -TTTAAAAAA-A
1 ATTTAAAAAATA
44426662 TATTTAAAAAAT-
1 -ATTTAAAAAATA
44426674 ATTTAAAAAA-A
1 ATTTAAAAAATA
44426685 TATTT----AA-A
1 -ATTTAAAAAATA
44426693 ATTTATAAAAATA
1 ATTTA-AAAAATA
44426706 ATTTAAAAATATA
1 ATTTAAAAA-ATA
44426719 TATTTAAAA
1 -ATTTAAAA
44426728 TCTACAAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 30
0.68 0.02 0.30
Matches are distributed among these distances:
7 4 0.06
8 3 0.04
9 2 0.03
10 5 0.07
11 10 0.14
12 26 0.38
13 11 0.16
14 8 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
ATTTAAAAAATA
Found at i:44426727 original size:34 final size:32
Alignment explanation
Indices: 44426615--44426748 Score: 119
Period size: 34 Copynumber: 4.1 Consensus size: 32
44426605 TTTAAATGCT
* *
44426615 AAATAATATTTAATATTTAAAAAATAATGTTTA
1 AAATAATATTTAAAATTTAAAAAATAAT-TTAA
** ***
44426648 AAATTTTAAAAAAATATTTAAAAAAT-ATTTAA
1 AAATAATATTTAAA-ATTTAAAAAATAATTTAA
44426680 AAA-AATATTTAAAATTTATAAAAATAATTTAA
1 AAATAATATTTAAAATTTA-AAAAATAATTTAA
* *
44426712 AAATATATATTTAAAATCTACAAAATATATTATAA
1 AAATA-ATATTTAAAATTTAAAAAATA-ATT-TAA
44426747 AA
1 AA
44426749 TATTTCAAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
30 5 0.06
31 11 0.14
32 15 0.19
33 17 0.21
34 27 0.34
35 5 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (32 bp):
AAATAATATTTAAAATTTAAAAAATAATTTAA
Found at i:44426728 original size:43 final size:42
Alignment explanation
Indices: 44426626--44426719 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 42
44426616 AATAATATTT
44426626 AATATTTAAAAAATAATGTTTAAAATTTTAAAAAAATATTTAAAA
1 AATATTTAAAAAAT-A--TTTAAAATTTTAAAAAAATATTTAAAA
*
44426671 AATATTTAAAAAAATATTTAAAA-TTTATAAAAATAATTTAAAA
1 AATATTT-AAAAAATATTTAAAATTTTAAAAAAAT-ATTTAAAA
44426714 ATATAT
1 A-ATAT
44426720 ATTTAAAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
42 10 0.22
43 16 0.36
44 4 0.09
45 8 0.18
46 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (42 bp):
AATATTTAAAAAATATTTAAAATTTTAAAAAAATATTTAAAA
Found at i:44426809 original size:14 final size:13
Alignment explanation
Indices: 44426792--44426827 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
44426782 TTAATCATAA
44426792 AAAATAAATAAAAT
1 AAAATAAAT-AAAT
44426806 AAAATAAATAAAT
1 AAAATAAATAAAT
44426819 AAAGATAAA
1 AAA-ATAAA
44426828 AGACAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:44426814 original size:18 final size:19
Alignment explanation
Indices: 44426793--44426828 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
44426783 TAATCATAAA
44426793 AAATAAATAAA-ATAAAAT
1 AAATAAATAAAGATAAAAT
44426811 AAATAAATAAAGATAAAA
1 AAATAAATAAAGATAAAA
44426829 GACAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (19 bp):
AAATAAATAAAGATAAAAT
Found at i:44426859 original size:25 final size:23
Alignment explanation
Indices: 44426826--44426876 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
44426816 AATAAAGATA
44426826 AAAGACAAAACATAAG-AAAAAAACG
1 AAAGACAAAA-A-AAGTAAAAAAA-G
*
44426851 AAAGTCAAAAAAAGTAAAAAAAG
1 AAAGACAAAAAAAGTAAAAAAAG
44426874 AAA
1 AAA
44426877 AAGAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
24 8 0.33
25 9 0.38
ACGTcount: A:0.75, C:0.08, G:0.12, T:0.06
Consensus pattern (23 bp):
AAAGACAAAAAAAGTAAAAAAAG
Found at i:44428555 original size:19 final size:17
Alignment explanation
Indices: 44428540--44428573 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44428530 GACATTTAGA
44428540 ATACAATAATACATTTG
1 ATACAATAATACATTTG
* *
44428557 GTATAATAATACATTTG
1 ATACAATAATACATTTG
44428574 GTCCTCAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
ATACAATAATACATTTG
Found at i:44429109 original size:41 final size:42
Alignment explanation
Indices: 44429061--44429142 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
44429051 GATACACATA
*
44429061 TTTTTATAATTTATAATTTATATTTTAAA-ATTTTTATAAAT
1 TTTTTATAATTTATAATTTAAATTTTAAATATTTTTATAAAT
* * **
44429102 TTTTTATATTTTTTCTTTTAAATTTTAAATATTTTTATAAA
1 TTTTTATAATTTATAATTTAAATTTTAAATATTTTTATAAA
44429143 AAATAGATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 24 0.69
42 11 0.31
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (42 bp):
TTTTTATAATTTATAATTTAAATTTTAAATATTTTTATAAAT
Found at i:44429408 original size:52 final size:52
Alignment explanation
Indices: 44429346--44429449 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
44429336 GGGTTTAGAT
44429346 AGTTTAAATTTGGATTGACTTCACAGGACTTGTTTTACTATTTAAAAATAGG
1 AGTTTAAATTTGGATTGACTTCACAGGACTTGTTTTACTATTTAAAAATAGG
*
44429398 AGTTTAAATTTGGATTGACTTCGCAGGACTTGTTTTACTATTTAAAAATAGG
1 AGTTTAAATTTGGATTGACTTCACAGGACTTGTTTTACTATTTAAAAATAGG
44429450 TTAAACTATA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (52 bp):
AGTTTAAATTTGGATTGACTTCACAGGACTTGTTTTACTATTTAAAAATAGG
Found at i:44431927 original size:30 final size:30
Alignment explanation
Indices: 44431883--44431945 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
44431873 ATTTAACAAG
44431883 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* * *
44431913 CAAATGTCTTTAAAATAATAACAAAGTTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
44431943 CAA
1 CAA
44431946 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:44433583 original size:8 final size:8
Alignment explanation
Indices: 44433570--44433594 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
44433560 ATTATATATA
44433570 TATTCTTT
1 TATTCTTT
44433578 TATTCTTT
1 TATTCTTT
44433586 TATTCTTT
1 TATTCTTT
44433594 T
1 T
44433595 GCATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTCTTT
Found at i:44434082 original size:24 final size:24
Alignment explanation
Indices: 44434055--44434106 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
44434045 TTAGTAAGTC
*
44434055 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
44434079 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
44434103 AAAT
1 AAAT
44434107 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:44436300 original size:3 final size:3
Alignment explanation
Indices: 44436292--44436350 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
44436282 AAATATTTAC
* * *
44436292 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TGT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44436340 TAT TAT TAT TA
1 TAT TAT TAT TA
44436351 CTATGAAGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:44436454 original size:23 final size:23
Alignment explanation
Indices: 44436422--44436473 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
44436412 TAGGTTTTCA
* * *
44436422 CTTATAATATTATTATTGTCATT
1 CTTATTATATGATTATTATCATT
*
44436445 CTTATTATATGGTTATTATCATT
1 CTTATTATATGATTATTATCATT
*
44436468 ATTATT
1 CTTATT
44436474 CTCACCATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.58
Consensus pattern (23 bp):
CTTATTATATGATTATTATCATT
Found at i:44436621 original size:20 final size:20
Alignment explanation
Indices: 44436584--44436621 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44436574 TTTTTGTTAC
*
44436584 TTATTTTTTTCATTGATTCT
1 TTATTTTTTTCATCGATTCT
44436604 TTATTTATTTT-ATCGATT
1 TTATTT-TTTTCATCGATT
44436622 ATTTTGTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.68
Consensus pattern (20 bp):
TTATTTTTTTCATCGATTCT
Found at i:44437691 original size:21 final size:24
Alignment explanation
Indices: 44437648--44437691 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
44437638 AAAATAGGAG
*
44437648 AAAACAATAAGAAAATAATATTTA
1 AAAACAATAAGAAAATAAGATTTA
44437672 AAAACAA-AA-AAAAT-AGATTT
1 AAAACAATAAGAAAATAAGATTT
44437692 TTTTGTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 2 0.11
24 7 0.37
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (24 bp):
AAAACAATAAGAAAATAAGATTTA
Found at i:44438186 original size:10 final size:10
Alignment explanation
Indices: 44438176--44438238 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
44438166 TATTTTCTTC
*
44438176 TGTTCTGTTC
1 TGTTCTGTTT
*
44438186 TGCTCTG-TT
1 TGTTCTGTTT
44438195 TGATT-TGTTT
1 TG-TTCTGTTT
44438205 TGTTCTGTTT
1 TGTTCTGTTT
*
44438215 TGTTTTGTTT
1 TGTTCTGTTT
44438225 TGTTC-GATTT
1 TGTTCTG-TTT
44438235 TGTT
1 TGTT
44438239 GCACTACCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.18
10 36 0.82
ACGTcount: A:0.03, C:0.10, G:0.21, T:0.67
Consensus pattern (10 bp):
TGTTCTGTTT
Found at i:44438218 original size:24 final size:25
Alignment explanation
Indices: 44438176--44438229 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
44438166 TATTTTCTTC
44438176 TGTTCTGTTCTGCTCTG-TTTGATT
1 TGTTCTGTTCTGCTCTGTTTTGATT
* * * *
44438200 TGTTTTGTTCTGTTTTGTTTTGTTT
1 TGTTCTGTTCTGCTCTGTTTTGATT
44438225 TGTTC
1 TGTTC
44438230 GATTTTGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.02, C:0.11, G:0.20, T:0.67
Consensus pattern (25 bp):
TGTTCTGTTCTGCTCTGTTTTGATT
Found at i:44438221 original size:20 final size:20
Alignment explanation
Indices: 44438189--44438238 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
44438179 TCTGTTCTGC
*
44438189 TCTG-TTTGATTTGTTTTGT
1 TCTGTTTTGTTTTGTTTTGT
44438208 TCTGTTTTGTTTTGTTTTGT
1 TCTGTTTTGTTTTGTTTTGT
44438228 TC-GATTTTGTT
1 TCTG-TTTTGTT
44438239 GCACTACCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.04, C:0.06, G:0.20, T:0.70
Consensus pattern (20 bp):
TCTGTTTTGTTTTGTTTTGT
Found at i:44438930 original size:39 final size:39
Alignment explanation
Indices: 44438882--44438965 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
44438872 GAAGTCTAGT
* *
44438882 TGAATCACATAAGTGCTAAACGGAAGACCGAAGGCTAAC
1 TGAAGCACATAAGTGATAAACGGAAGACCGAAGGCTAAC
*
44438921 TGAAGCACATAAGTGATAAACGGAAGCCCGAAGGCTAAC
1 TGAAGCACATAAGTGATAAACGGAAGACCGAAGGCTAAC
44438960 TGAAGC
1 TGAAGC
44438966 TCATTAAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.14
Consensus pattern (39 bp):
TGAAGCACATAAGTGATAAACGGAAGACCGAAGGCTAAC
Found at i:44441931 original size:21 final size:20
Alignment explanation
Indices: 44441881--44441931 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
44441871 TTTTAGTCAC
*
44441881 TTAATTATTAATTTTTTCAA
1 TTAATTATTAATTTTTTAAA
44441901 TATAATTATTAAATTTTTTAAA
1 T-TAATTATT-AATTTTTTAAA
*
44441923 TTAAATATT
1 TTAATTATT
44441932 TTGGTCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 15 0.56
22 11 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATTATTAATTTTTTAAA
Found at i:44442979 original size:29 final size:28
Alignment explanation
Indices: 44442923--44442980 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
44442913 TGTACATAAG
* *
44442923 ATAACATAAAAATATATATACCACTAAT
1 ATAACATAAAAATACATATACAACTAAT
*
44442951 ATAACATAAAAAATACATATACAATTAAT
1 ATAACAT-AAAAATACATATACAACTAAT
44442980 A
1 A
44442981 ATATGAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAACATAAAAATACATATACAACTAAT
Found at i:44443664 original size:25 final size:25
Alignment explanation
Indices: 44443606--44443668 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
44443596 ATACATGATA
*
44443606 ATATATAATA-ATATTAGAAAATAT
1 ATATATAATATACATTAGAAAATAT
*
44443630 ATGTACATAATATACA-TATGAAAATAT
1 A--TATATAATATACATTA-GAAAATAT
44443657 ATATATAATATA
1 ATATATAATATA
44443669 GTATCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.03
25 10 0.31
26 10 0.31
27 11 0.34
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (25 bp):
ATATATAATATACATTAGAAAATAT
Found at i:44445351 original size:23 final size:23
Alignment explanation
Indices: 44445325--44445375 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
44445315 ACTTGAAATG
44445325 TATATTTGAAATATTTTATAATATA
1 TATATTTGAAA-ATTTTA-AATATA
**
44445350 TATATTTTTAAATTTTAAATATA
1 TATATTTGAAAATTTTAAATATA
44445373 TAT
1 TAT
44445376 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 6 0.25
25 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATATTTGAAAATTTTAAATATA
Found at i:44445373 original size:19 final size:19
Alignment explanation
Indices: 44445349--44445458 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 19
44445339 TTTATAATAT
*
44445349 ATATATTTTTAAATTTTAA
1 ATATATTTTTAAATATTAA
*
44445368 ATATATATTTTTAA-ATT--
1 ATATAT-TTTTAAATATTAA
*
44445385 AT-T-TTTCTAAAT-TTCAA
1 ATATATTTTTAAATATT-AA
44445402 ATATTACTTTTTAAATATTAA
1 ATA-TA-TTTTTAAATATTAA
*
44445423 ATATATTTTTAAATAATAA
1 ATATATTTTTAAATATTAA
44445442 ATATTATTTTTAAATAT
1 ATA-TATTTTTAAATAT
44445459 ATTTTAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
14 7 0.10
15 1 0.01
16 1 0.01
17 4 0.05
19 25 0.34
20 20 0.27
21 13 0.18
22 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTTTTAAATATTAA
Found at i:44445398 original size:34 final size:35
Alignment explanation
Indices: 44445335--44445460 Score: 109
Period size: 34 Copynumber: 3.5 Consensus size: 35
44445325 TATATTTGAA
*
44445335 ATATTTTATAATATATATATTTTTAAATTTTAAATAT
1 ATATTTT-TAA-ATATATATTTTTAAATTTCAAATAT
44445372 ATATTTTTAAAT-TAT-TTTTCTAAATTTCAAATAT
1 ATATTTTTAAATATATATTTT-TAAATTTCAAATAT
*
44445406 -TACTTTTTAAATATTAAATATATTTTTAAATAAT-AAATAT
1 ATA-TTTTT-AA-A-T--ATATATTTTTAAAT-TTCAAATAT
44445446 -TATTTTTAAATATAT
1 ATATTTTTAAATATAT
44445461 TTTAAATATT
Statistics
Matches: 77, Mismatches: 2, Indels: 23
0.75 0.02 0.23
Matches are distributed among these distances:
33 6 0.08
34 25 0.32
35 4 0.05
36 5 0.06
37 9 0.12
38 2 0.03
39 5 0.06
40 16 0.21
41 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (35 bp):
ATATTTTTAAATATATATTTTTAAATTTCAAATAT
Found at i:44445436 original size:12 final size:12
Alignment explanation
Indices: 44445419--44445487 Score: 60
Period size: 13 Copynumber: 6.0 Consensus size: 12
44445409 TTTTTAAATA
44445419 TTAAATATATTT
1 TTAAATATATTT
44445431 TTAAATA-A---
1 TTAAATATATTT
44445439 -TAAATATTATTT
1 TTAAATA-TATTT
44445451 TTAAATATA-TT
1 TTAAATATATTT
*
44445462 TTAAATATTGTTT
1 TTAAATA-TATTT
44445475 TTAAATAATATTT
1 TTAAAT-ATATTT
44445488 AATTTTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
7 6 0.13
9 1 0.02
11 10 0.22
12 10 0.22
13 18 0.39
14 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (12 bp):
TTAAATATATTT
Found at i:44445449 original size:20 final size:20
Alignment explanation
Indices: 44445400--44445484 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 20
44445390 TCTAAATTTC
*
44445400 AAATATTACTTTTTAAATATT
1 AAATATTA-TTTTTAAATAAT
44445421 AAATA-TATTTTTAAATAAT
1 AAATATTATTTTTAAATAAT
44445440 AAATATTATTTTTAAATATATTTT
1 AAATATTATTTTTAAATA-A---T
*
44445464 AAATATTGTTTTTAAATAAT
1 AAATATTATTTTTAAATAAT
44445484 A
1 A
44445485 TTTAATTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
19 16 0.28
20 16 0.28
21 6 0.11
23 1 0.02
24 18 0.32
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
AAATATTATTTTTAAATAAT
Found at i:44445457 original size:13 final size:13
Alignment explanation
Indices: 44445439--44445487 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
44445429 TTTTAAATAA
44445439 TAAATATTATTTT
1 TAAATATTATTTT
44445452 TAAATA-TA-TTT
1 TAAATATTATTTT
*
44445463 TAAATATTGTTTT
1 TAAATATTATTTT
*
44445476 TAAATAATATTT
1 TAAATATTATTT
44445488 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 9 0.29
12 3 0.10
13 19 0.61
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TAAATATTATTTT
Found at i:44445475 original size:24 final size:25
Alignment explanation
Indices: 44445362--44445487 Score: 86
Period size: 24 Copynumber: 5.6 Consensus size: 25
44445352 TATTTTTAAA
*
44445362 TTTTAAATATATATTTTTAA-ATTAT
1 TTTTAAATA-ATATTTTAAATATTAT
* *
44445387 TTTT--CTAA-ATTTCAAATATTACT
1 TTTTAAATAATATTTTAAATATTA-T
44445410 TTTT--A-AATA--TTAAATA-TAT
1 TTTTAAATAATATTTTAAATATTAT
44445429 TTTTAAAT-A-A---TAAATATTAT
1 TTTTAAATAATATTTTAAATATTAT
*
44445449 TTTTAAAT-ATATTTTAAATATTGT
1 TTTTAAATAATATTTTAAATATTAT
44445473 TTTTAAATAATATTT
1 TTTTAAATAATATTT
44445488 AATTTTTAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 24
0.73 0.05 0.21
Matches are distributed among these distances:
19 11 0.13
20 15 0.18
21 15 0.18
22 7 0.08
23 8 0.10
24 17 0.20
25 10 0.12
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (25 bp):
TTTTAAATAATATTTTAAATATTAT
Found at i:44445495 original size:18 final size:19
Alignment explanation
Indices: 44445472--44445509 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
44445462 TTAAATATTG
44445472 TTTTT-AAATAATATTTAA
1 TTTTTAAAATAATATTTAA
44445490 TTTTTAAAAATAATATTTAA
1 TTTTT-AAAATAATATTTAA
44445510 AATTTAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAAATAATATTTAA
Found at i:44445509 original size:44 final size:44
Alignment explanation
Indices: 44445415--44445510 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
44445405 TTACTTTTTA
*
44445415 AATA-TTAAATATATTTTTAAATAATAAATATTATTTTTAAATAT
1 AATATTTAAATATATTTTTAAATAAT-AATATTATTTTTAAAAAT
*
44445459 -AT-TTTAAATATTGTTTTTAAATAAT-AT-TTAATTTTTAAAAAT
1 AATATTTAAATA-TATTTTTAAATAATAATATT-ATTTTTAAAAAT
44445501 AATATTTAAA
1 AATATTTAAA
44445511 ATTTAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
41 2 0.04
42 13 0.29
43 11 0.24
44 19 0.42
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (44 bp):
AATATTTAAATATATTTTTAAATAATAATATTATTTTTAAAAAT
Found at i:44445515 original size:20 final size:20
Alignment explanation
Indices: 44445477--44445532 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
44445467 TATTGTTTTT
**
44445477 AAATAATATTTAATTTTTAA
1 AAATAATATTTAAAATTTAA
*
44445497 AAATAATATTTAAAATTTAG
1 AAATAATATTTAAAATTTAA
44445517 AAA-AATACTTTAAAAT
1 AAATAATA-TTTAAAAT
44445533 ATATATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATAATATTTAAAATTTAA
Found at i:44445520 original size:22 final size:20
Alignment explanation
Indices: 44445477--44445523 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
44445467 TATTGTTTTT
**
44445477 AAATAATATTTAATTTTTAA
1 AAATAATATTTAATTTAGAA
44445497 AAATAATATTTAAAATTTAGAA
1 AAATAATATTT--AATTTAGAA
44445519 AAATA
1 AAATA
44445524 CTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATAATATTTAATTTAGAA
Found at i:44445551 original size:9 final size:9
Alignment explanation
Indices: 44445537--44445579 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
44445527 TAAAATATAT
44445537 ATATTTAAA
1 ATATTTAAA
44445546 ATATTTAAAA
1 ATATTT-AAA
44445556 TATATTATAAA
1 -ATATT-TAAA
*
44445567 ATATTTCAA
1 ATATTTAAA
44445576 ATAT
1 ATAT
44445580 ACATTTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 13 0.43
10 8 0.27
11 8 0.27
12 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATTTAAA
Found at i:44445627 original size:14 final size:14
Alignment explanation
Indices: 44445608--44445647 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
44445598 AATTAATCAT
*
44445608 AAATAAGATAAATA
1 AAATAAAATAAATA
44445622 AAATAAAATAAAT-
1 AAATAAAATAAATA
44445635 AAATAAACATAAA
1 AAATAAA-ATAAA
44445648 AGAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:44445636 original size:18 final size:19
Alignment explanation
Indices: 44445608--44445657 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
44445598 AATTAATCAT
44445608 AAATAAGATAAATAAA-ATA
1 AAATAA-ATAAATAAACATA
44445627 AAATAAATAAATAAACATA
1 AAATAAATAAATAAACATA
*
44445646 AAAGAAA-AAATA
1 AAATAAATAAATA
44445658 TAAAAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (19 bp):
AAATAAATAAATAAACATA
Found at i:44445675 original size:23 final size:23
Alignment explanation
Indices: 44445645--44445721 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
44445635 AAATAAACAT
44445645 AAAAGAAAAAATATAAAAAAAAG
1 AAAAGAAAAAATATAAAAAAAAG
* *
44445668 AAAAGAAAAGATAGT-CAAAAAAG
1 AAAAGAAAAAATA-TAAAAAAAAG
* * *
44445691 TAAA-AAAAAGTAAAAAAGAAAAG
1 AAAAGAAAAAATATAAAA-AAAAG
44445714 AAAAGAAA
1 AAAAGAAA
44445722 GTAACAGCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
22 8 0.19
23 30 0.71
24 4 0.10
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.08
Consensus pattern (23 bp):
AAAAGAAAAAATATAAAAAAAAG
Found at i:44445717 original size:18 final size:19
Alignment explanation
Indices: 44445668--44445718 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
44445658 TAAAAAAAAG
*
44445668 AAAAGAAAAG-ATAGTCAA
1 AAAAGAAAAGAAAAGTCAA
44445686 AAAAGTAAAA-AAAAGT-AA
1 AAAAG-AAAAGAAAAGTCAA
44445704 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
44445719 AAAGTAACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 4 0.14
18 17 0.59
19 8 0.28
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAAGAAAAGAAAAGTCAA
Found at i:44446724 original size:9 final size:9
Alignment explanation
Indices: 44446712--44446736 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
44446702 TTTTTCTTAT
44446712 TTTATTTTG
1 TTTATTTTG
44446721 TTTATTTTG
1 TTTATTTTG
44446730 TTTATTT
1 TTTATTT
44446737 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTATTTTG
Found at i:44446819 original size:23 final size:21
Alignment explanation
Indices: 44446780--44446836 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
44446770 TATTTGAAAT
*
44446780 ATTTTATAATATAATTTTTTTTAA
1 ATTTTA-AATATAA--TTTTTAAA
*
44446804 ATTTTAAATATTATTTTTAAA
1 ATTTTAAATATAATTTTTAAA
44446825 ATTTTAAATATA
1 ATTTTAAATATA
44446837 TATATATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.60
23 6 0.20
24 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTAAATATAATTTTTAAA
Found at i:44446837 original size:23 final size:23
Alignment explanation
Indices: 44446780--44446851 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
44446770 TATTTGAAAT
*
44446780 ATTTTATAATATAATT-TTTTTTAA
1 ATTTTA-AATAT-ATTATTTTTAAA
44446804 ATTTT-AA-ATATTATTTTTAAA
1 ATTTTAAATATATTATTTTTAAA
* *
44446825 ATTTTAAATATATATATATTTGAA
1 ATTTTAAATATAT-TATTTTTAAA
44446849 ATT
1 ATT
44446852 ATTTCTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.07
21 14 0.34
22 4 0.10
23 4 0.10
24 16 0.39
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
ATTTTAAATATATTATTTTTAAA
Found at i:44446891 original size:22 final size:22
Alignment explanation
Indices: 44446851--44446911 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
44446841 TATTTGAAAT
*
44446851 TATTTCTTATAAATTTTAAATATA
1 TATTT-TT-TAAATATTAAATATA
44446875 TATTTTTTAAATATTAAATATA
1 TATTTTTTAAATATTAAATATA
*
44446897 T-TTTTTAATAATATT
1 TATTTTTTA-AATATT
44446912 TAAACATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.18
22 21 0.62
23 2 0.06
24 5 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTTTTAAATATTAAATATA
Found at i:44447069 original size:12 final size:13
Alignment explanation
Indices: 44447054--44447083 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
44447044 TTTTTAAATT
44447054 TTTTA-TTAAAAA
1 TTTTATTTAAAAA
44447066 TTTTATTTAAAAA
1 TTTTATTTAAAAA
44447079 TTTTA
1 TTTTA
44447084 AATGTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTATTTAAAAA
Found at i:44447184 original size:20 final size:20
Alignment explanation
Indices: 44447159--44447202 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
44447149 TTAAATGTTT
44447159 AAATGT-TTCATATTATTAAA
1 AAATGTATT-ATATTATTAAA
* *
44447179 AAATGTATTTTATTTTTAAA
1 AAATGTATTATATTATTAAA
44447199 AAAT
1 AAAT
44447203 AATATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
AAATGTATTATATTATTAAA
Found at i:44447231 original size:21 final size:22
Alignment explanation
Indices: 44447192--44447233 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
44447182 TGTATTTTAT
44447192 TTTTAAAAAATAATATTTAAAA
1 TTTTAAAAAATAATATTTAAAA
44447214 TTTTAAAAAATAAT-TTTAAA
1 TTTTAAAAAATAATATTTAAA
44447234 TATATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAAAATAATATTTAAAA
Found at i:44447234 original size:20 final size:20
Alignment explanation
Indices: 44447174--44447234 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
44447164 TTTCATATTA
* *
44447174 TTAAAAAATGTATTTT-ATTT
1 TTAAAAAAT-AATTTTAAATT
44447194 TTAAAAAATAATATTTAAAATT
1 TTAAAAAATAAT-TTT-AAATT
44447216 TTAAAAAATAATTTTAAAT
1 TTAAAAAATAATTTTAAAT
44447235 ATATATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 16 0.44
21 3 0.08
22 15 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TTAAAAAATAATTTTAAATT
Found at i:44447243 original size:35 final size:33
Alignment explanation
Indices: 44447198--44447294 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 33
44447188 TTATTTTTAA
44447198 AAAATAATATTTAAAATTTTAAAAAATAATTTT
1 AAAATAATATTTAAAATTTTAAAAAATAATTTT
44447231 AAATATATATATTTAAAATTTTAAAAAAATAATTTT
1 AAA-ATA-ATATTTAAAATTTT-AAAAAATAATTTT
44447267 AAAATAATATTTAAAATTTTAAAAAATA
1 AAAATAATATTTAAAATTTTAAAAAATA
44447295 TATATTATAA
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 11 0.18
34 17 0.28
35 17 0.28
36 16 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
AAAATAATATTTAAAATTTTAAAAAATAATTTT
Found at i:44447267 original size:22 final size:22
Alignment explanation
Indices: 44447225--44447271 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
44447215 TTTAAAAAAT
* *
44447225 AATTTTAAATATATATATTTAA
1 AATTTTAAAAAAATATATTTAA
44447247 AATTTTAAAAAAATA-ATTTTAA
1 AATTTTAAAAAAATATA-TTTAA
44447269 AAT
1 AAT
44447272 AATATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTTAAAAAAATATATTTAA
Found at i:44447324 original size:13 final size:13
Alignment explanation
Indices: 44447306--44447332 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44447296 ATATTATAAA
44447306 ACATTTCAAATTT
1 ACATTTCAAATTT
44447319 ACATTTCAAATTT
1 ACATTTCAAATTT
44447332 A
1 A
44447333 TTAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (13 bp):
ACATTTCAAATTT
Found at i:44447353 original size:4 final size:4
Alignment explanation
Indices: 44447344--44447379 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
44447334 TAAAATTAAT
44447344 AATA AATAA AATA AATA AATA AATA AATAA AATA AA
1 AATA AAT-A AATA AATA AATA AATA AAT-A AATA AA
44447380 ATAAGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 22 0.73
5 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:44447355 original size:16 final size:17
Alignment explanation
Indices: 44447334--44447379 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
44447324 TCAAATTTAT
*
44447334 TAAAATTAAT-AATAAA
1 TAAAATAAATAAATAAA
44447350 TAAAATAAATAAATAAA
1 TAAAATAAATAAATAAA
44447367 T-AAATAAAATAAA
1 TAAAAT-AAATAAA
44447380 ATAAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAAATAAATAAA
Found at i:44447358 original size:21 final size:22
Alignment explanation
Indices: 44447334--44447383 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
44447324 TCAAATTTAT
*
44447334 TAAAATTAAT-AATAAATAAAA
1 TAAAATAAATAAATAAATAAAA
44447355 T-AAATAAATAAATAAATAAAA
1 TAAAATAAATAAATAAATAAAA
44447376 TAAAATAA
1 TAAAATAA
44447384 GAAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 13 0.50
22 6 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAAATAAATAAATAAATAAAA
Found at i:44447413 original size:8 final size:8
Alignment explanation
Indices: 44447347--44447415 Score: 59
Period size: 8 Copynumber: 8.5 Consensus size: 8
44447337 AATTAATAAT
44447347 AAATAAAA
1 AAATAAAA
*
44447355 TAAATAAAT
1 -AAATAAAA
44447364 AAATAAATA
1 AAATAAA-A
44447373 AAATAAAA
1 AAATAAAA
* *
44447381 TAA-GAAA
1 AAATAAAA
*
44447388 AAATATAA
1 AAATAAAA
* *
44447396 AACTTAAA
1 AAATAAAA
44447404 AAATAAAA
1 AAATAAAA
44447412 AAAT
1 AAAT
44447416 TAAAGAACAA
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
7 5 0.11
8 27 0.59
9 14 0.30
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (8 bp):
AAATAAAA
Found at i:44447438 original size:20 final size:21
Alignment explanation
Indices: 44447401--44447466 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
44447391 TATAAAACTT
44447401 AAAAAA-TAAAAAAA-TTAAA
1 AAAAAAGTAAAAAAATTTAAA
* * *
44447420 GAACAAG-AAAAAATTTTAAA
1 AAAAAAGTAAAAAAATTTAAA
44447440 AAAAAAGTAAAAAAATTTAAA
1 AAAAAAGTAAAAAAATTTAAA
44447461 AAAAAA
1 AAAAAA
44447467 TCAGAAGCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 10 0.26
20 10 0.26
21 18 0.47
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAAAGTAAAAAAATTTAAA
Found at i:44447644 original size:13 final size:11
Alignment explanation
Indices: 44447613--44447651 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 11
44447603 ATTTAAACCT
44447613 TTTTA-AAAAA
1 TTTTATAAAAA
44447623 TTTTATAAAAA
1 TTTTATAAAAA
44447634 TTTTATTTAAAAA
1 TTTTA--TAAAAA
44447647 TTTTA
1 TTTTA
44447652 AATGTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.19
11 10 0.38
13 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTATAAAAA
Found at i:44447667 original size:30 final size:31
Alignment explanation
Indices: 44447630--44447711 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 31
44447620 AAATTTTATA
*
44447630 AAAATTTTATTTAAAA-AT-TTTAA-ATGTTT
1 AAAATTTTATTAAAAATATATTTAATAT-TTT
44447659 AAATATTTT-TTAAAAATATATTTAATATTTT
1 AAA-ATTTTATTAAAAATATATTTAATATTTT
44447690 AAAATTTTA--AAAAATA-ATTTAA
1 AAAATTTTATTAAAAATATATTTAA
44447712 AAATAATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
28 6 0.13
29 16 0.34
30 12 0.26
31 11 0.23
32 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
AAAATTTTATTAAAAATATATTTAATATTTT
Found at i:44447691 original size:20 final size:20
Alignment explanation
Indices: 44447666--44447742 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
44447656 TTTAAATATT
44447666 TTTTAAAAATATATTTAATA
1 TTTTAAAAATATATTTAATA
* * ***
44447686 TTTTAAAATTTTAAAAAATA
1 TTTTAAAAATATATTTAATA
*
44447706 ATTTAAAAATAATATTTAATA
1 TTTTAAAAAT-ATATTTAATA
44447727 TTTTAAAATATATATT
1 TTTTAAAA-ATATATT
44447743 ATAAAATATT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
20 23 0.53
21 18 0.42
22 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTAAAAATATATTTAATA
Found at i:44447726 original size:21 final size:20
Alignment explanation
Indices: 44447667--44447742 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 20
44447657 TTAAATATTT
44447667 TTTAAAAAT-ATATTTAATA
1 TTTAAAAATAATATTTAATA
* ** ***
44447686 TTTTAAAATTTTAAAAAATAA
1 TTTAAAAATAATATTTAAT-A
44447707 TTTAAAAATAATATTTAATA
1 TTTAAAAATAATATTTAATA
*
44447727 TTTTAAAATATATATT
1 TTTAAAAATA-ATATT
44447743 ATAAAATATT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 8 0.19
20 15 0.36
21 19 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAAATAATATTTAATA
Found at i:44447730 original size:33 final size:36
Alignment explanation
Indices: 44447681--44447748 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 36
44447671 AAAATATATT
44447681 TAATATTTTAAAATTTTAAAAAATA-ATT-TAAAAA
1 TAATATTTTAAAATTTTAAAAAATATATTATAAAAA
* *
44447715 TAATA-TTTAATATTTTAAAATATATATTATAAAA
1 TAATATTTTAAAATTTTAAAAAATATATTATAAAA
44447749 TATTTCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 17 0.57
34 8 0.27
35 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
TAATATTTTAAAATTTTAAAAAATATATTATAAAAA
Found at i:44447781 original size:23 final size:23
Alignment explanation
Indices: 44447727--44447781 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
44447717 ATATTTAATA
*
44447727 TTTTAAAATATATATTATAAAAT
1 TTTTAAAATATACATTATAAAAT
* * *
44447750 ATTTCAAATATACATT-TCAAATT
1 TTTTAAAATATACATTAT-AAAAT
44447773 TTTTAAAAT
1 TTTTAAAAT
44447782 TAATAACAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTAAAATATACATTATAAAAT
Found at i:44447866 original size:19 final size:18
Alignment explanation
Indices: 44447842--44447886 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
44447832 TATAAAACTT
44447842 AAAAAAAGAAAAAAATTA
1 AAAAAAAGAAAAAAATTA
* *
44447860 AAGAAAAAGACAAAAGTTA
1 AA-AAAAAGAAAAAAATTA
44447879 AAAAAAAG
1 AAAAAAAG
44447887 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (18 bp):
AAAAAAAGAAAAAAATTA
Found at i:44447885 original size:37 final size:39
Alignment explanation
Indices: 44447823--44447895 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
44447813 AAAATAAAAT
*
44447823 AAGAAAAAGTATAAAACTTAAAAAAAG-AA-AAAAATTA
1 AAGAAAAAGTACAAAACTTAAAAAAAGTAATAAAAATTA
*
44447860 AAGAAAAAG-ACAAAAGTTAAAAAAAAGTAATAAAAA
1 AAGAAAAAGTACAAAACTT-AAAAAAAGTAATAAAAA
44447896 ATTAGAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 7 0.23
37 17 0.55
38 2 0.06
39 5 0.16
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.14
Consensus pattern (39 bp):
AAGAAAAAGTACAAAACTTAAAAAAAGTAATAAAAATTA
Found at i:44462783 original size:7 final size:7
Alignment explanation
Indices: 44462771--44462811 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
44462761 TTCGGGTGCT
44462771 ATAGCCA
1 ATAGCCA
44462778 ATAGCCA
1 ATAGCCA
44462785 ATAGCCA
1 ATAGCCA
44462792 ATAGCCA
1 ATAGCCA
44462799 ATAGCCA
1 ATAGCCA
44462806 ATAGCC
1 ATAGCC
44462812 CCCTCGCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (7 bp):
ATAGCCA
Found at i:44465735 original size:32 final size:32
Alignment explanation
Indices: 44465698--44465762 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
44465688 GGGCTAGTTG
44465698 ACAAAAGCAATTAATCAAGATGCTCATAGAAT
1 ACAAAAGCAATTAATCAAGATGCTCATAGAAT
*
44465730 ACAAAAGCAATTAGTCAAGATGCTCATAGAAT
1 ACAAAAGCAATTAATCAAGATGCTCATAGAAT
44465762 A
1 A
44465763 AACATTATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (32 bp):
ACAAAAGCAATTAATCAAGATGCTCATAGAAT
Found at i:44468498 original size:105 final size:105
Alignment explanation
Indices: 44468350--44468551 Score: 271
Period size: 105 Copynumber: 1.9 Consensus size: 105
44468340 AACATCAGGC
* * *
44468350 TCAATGCCTCGTTTTATCATTGTGTCAACAATATCCTCAGCTTTAGAAACCATCCCTTCTTTGCA
1 TCAATGCCTCGCTTTATCATCGTGTCAACAATATCCTCAGCTTTAGAAACCATCCCTTCTGTGCA
* *
44468415 ACGTGCATCAACCAACGTAGTATACGTGACAACATTGGGT
66 AAGTGCATCAACCAACATAGTATACGTGACAACATTGGGT
* * * * * *
44468455 TCAATGCCTTGCTTTCTCATCGTGTCAACGATCT-CTACAGCTTTAGAAATCATTCCTTCTGTGC
1 TCAATGCCTCGCTTTATCATCGTGTCAACAATATCCT-CAGCTTTAGAAACCATCCCTTCTGTGC
* *
44468519 AAAGTGCATCAATCAATATAGTATACGTGACAA
65 AAAGTGCATCAACCAACATAGTATACGTGACAA
44468552 TATCAAGTGA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 2 0.02
105 81 0.98
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (105 bp):
TCAATGCCTCGCTTTATCATCGTGTCAACAATATCCTCAGCTTTAGAAACCATCCCTTCTGTGCA
AAGTGCATCAACCAACATAGTATACGTGACAACATTGGGT
Found at i:44474986 original size:23 final size:23
Alignment explanation
Indices: 44474956--44475007 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
44474946 TTCTATGCAC
* *
44474956 GCAAGTGATAGTGGCACTACGAT
1 GCAAGTGAAAGCGGCACTACGAT
* *
44474979 GCAAGTGAAAGCGGCACTATGGT
1 GCAAGTGAAAGCGGCACTACGAT
44475002 GCAAGT
1 GCAAGT
44475008 TTGAGTGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (23 bp):
GCAAGTGAAAGCGGCACTACGAT
Found at i:44485405 original size:1 final size:1
Alignment explanation
Indices: 44485401--44485432 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
44485391 CCCCAAAACC
44485401 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44485433 TTATGTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44485950 original size:29 final size:29
Alignment explanation
Indices: 44485905--44485992 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
44485895 AAATAGGTAT
*
44485905 TGCTTTCAACATTGTAATACATCACCTCC
1 TGCTTTCAACATCGTAATACATCACCTCC
*
44485934 TGCTTTCAACATCGTAATACATCAGCTCC
1 TGCTTTCAACATCGTAATACATCACCTCC
44485963 TGCTTTCAACATCGTAATACATCACCTCC
1 TGCTTTCAACATCGTAATACATCACCTCC
44485992 T
1 T
44485993 TTCTTTTCCA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.33
Consensus pattern (29 bp):
TGCTTTCAACATCGTAATACATCACCTCC
Found at i:44487286 original size:20 final size:20
Alignment explanation
Indices: 44487258--44487295 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44487248 AATGGAAGGG
* *
44487258 TTTTTATATGAATTTTAATC
1 TTTTGATATGAAGTTTAATC
44487278 TTTTGATATGAAGTTTAA
1 TTTTGATATGAAGTTTAA
44487296 ATTTGATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTGATATGAAGTTTAATC
Found at i:44488299 original size:45 final size:45
Alignment explanation
Indices: 44488233--44488330 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
44488223 TAAGGTATGT
* *
44488233 TTTTTACTCGTCAATAGGTAATGGTCCATCGTAGCAATCGTTGAA
1 TTTTTACTCGTCAATAGGTAATGATCCATCGTACCAATCGTTGAA
* *
44488278 TTTTTATTCGTCAATTA-GTAATGATTCATCGTACCAATCGTTGAA
1 TTTTTACTCGTCAA-TAGGTAATGATCCATCGTACCAATCGTTGAA
*
44488323 TTGTTACT
1 TTTTTACT
44488331 TGGAGCTCGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 44 0.96
46 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (45 bp):
TTTTTACTCGTCAATAGGTAATGATCCATCGTACCAATCGTTGAA
Found at i:44490958 original size:276 final size:277
Alignment explanation
Indices: 44490455--44491008 Score: 1002
Period size: 276 Copynumber: 2.0 Consensus size: 277
44490445 GAAAAGACTC
*
44490455 GATTTCTGATTTTTTGCCTTTTCTGCACTTCTGTTTCTTTCTGTGCCTTTACATCTTCTGTTACT
1 GATTTCTGATTTTTTGCCTTTTCTGCACTTCTGTTCCTTTCTGTGCCTTTACATCTTCTGTTACT
* * *
44490520 TCAAGGGTATAATGCACAGTGCAATAAAGTCGCCCGAGTAAGCAACTCAGGCAAGTTCTGGTTAA
66 TCAAAGGTATAATGCACAGTGCAATAAAGTCGCCCGAGTAAGCAACGCAGGCAAGTTCTGATTAA
* * *
44490585 ATCTTTCTTTTGTTATAACGAAAGCTGCATATGCTGAGATCAAATCCCAAATCTGCTAGATACCG
131 ATCTTCCTTTTGTTATAACGAAAGCTGCATATGCTGAGATCAAACCCCAAATCTGCTAGATACCA
*
44490650 CCTCATAAAGGTGGTTGCAAGAACCAGCGGGCTAAGCCGTGGGTTCGGATTAGATGCTTCAATAT
196 CCTCATAAAGGTGGTTGCAAGAACCAGCGGGCTAAGCAGTGGGTTCGGATTAGATGCTTCAATAT
44490715 TCATAATGTTCCATGAA
261 TCATAATGTTCCATGAA
44490732 GATTTCTGA-TTTTTGCCTTTTCTGCACTTCTGTTCCTTTCTGTGCCTTTACATCTTCTGTTACT
1 GATTTCTGATTTTTTGCCTTTTCTGCACTTCTGTTCCTTTCTGTGCCTTTACATCTTCTGTTACT
44490796 TCAAAGGTATAATGCACAGTGCAATAAAGTCGCCCGAGTAAGCAACGCAGGCAAGTTCTGATTAA
66 TCAAAGGTATAATGCACAGTGCAATAAAGTCGCCCGAGTAAGCAACGCAGGCAAGTTCTGATTAA
44490861 ATCTTCCTTTTGTTATAACGAAAGCTGCATATGCTGAGATCAAACCCCAAATCTGCTAGATACCA
131 ATCTTCCTTTTGTTATAACGAAAGCTGCATATGCTGAGATCAAACCCCAAATCTGCTAGATACCA
* *
44490926 CCTCATAAAGGTGGTTGCAAGAACCAGCGGGCTAAGCATTGGGTTCGGATTAGATGGTTCAATAT
196 CCTCATAAAGGTGGTTGCAAGAACCAGCGGGCTAAGCAGTGGGTTCGGATTAGATGCTTCAATAT
*
44490991 TTATAATGTTCCATGAA
261 TCATAATGTTCCATGAA
44491008 G
1 G
44491009 TGTCTAATGG
Statistics
Matches: 266, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
276 257 0.97
277 9 0.03
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (277 bp):
GATTTCTGATTTTTTGCCTTTTCTGCACTTCTGTTCCTTTCTGTGCCTTTACATCTTCTGTTACT
TCAAAGGTATAATGCACAGTGCAATAAAGTCGCCCGAGTAAGCAACGCAGGCAAGTTCTGATTAA
ATCTTCCTTTTGTTATAACGAAAGCTGCATATGCTGAGATCAAACCCCAAATCTGCTAGATACCA
CCTCATAAAGGTGGTTGCAAGAACCAGCGGGCTAAGCAGTGGGTTCGGATTAGATGCTTCAATAT
TCATAATGTTCCATGAA
Found at i:44492006 original size:20 final size:20
Alignment explanation
Indices: 44491981--44492018 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44491971 TGACATGTGT
44491981 GTTTTTTTCATTTT-TTTCGA
1 GTTTTTTT-ATTTTATTTCGA
44492001 GTTTTTTTATTTTATTTC
1 GTTTTTTTATTTTATTTC
44492019 TCAAGGCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.11, C:0.08, G:0.08, T:0.74
Consensus pattern (20 bp):
GTTTTTTTATTTTATTTCGA
Found at i:44494112 original size:22 final size:23
Alignment explanation
Indices: 44494087--44494130 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
44494077 CAACAATTTA
44494087 ATAAATATATAAATTT-ATTATC
1 ATAAATATATAAATTTAATTATC
*
44494109 ATAAATATATAATTTTAATTAT
1 ATAAATATATAAATTTAATTAT
44494131 TATTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAATATATAAATTTAATTATC
Found at i:44499647 original size:35 final size:35
Alignment explanation
Indices: 44499608--44499674 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
44499598 GTGAGAAATG
* *
44499608 TATTT-TTTTATTAA-ATTAAATTTAATACTTTTTTA
1 TATTTATTTT-TTAAGA-TAAAATTAAAACTTTTTTA
44499643 TATTTATTTTTTAAGATAAAATTAAAACTTTT
1 TATTTATTTTTTAAGATAAAATTAAAACTTTT
44499675 GAAATTAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 23 0.82
36 5 0.18
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (35 bp):
TATTTATTTTTTAAGATAAAATTAAAACTTTTTTA
Found at i:44500099 original size:23 final size:24
Alignment explanation
Indices: 44500073--44500119 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
44500063 ATATCTCAAT
44500073 TTAATT-TAATTTAATTC-AATTAA
1 TTAATTGTAA-TTAATTCTAATTAA
*
44500096 TTAATTGTGATTAATTCTAATTAA
1 TTAATTGTAATTAATTCTAATTAA
44500120 ACTTATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (24 bp):
TTAATTGTAATTAATTCTAATTAA
Found at i:44503475 original size:16 final size:16
Alignment explanation
Indices: 44503453--44503494 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
44503443 TTTTTGTGTT
44503453 ATTTTAATATTAAATA
1 ATTTTAATATTAAATA
* *
44503469 TTTTTAAAATTAAATA
1 ATTTTAATATTAAATA
*
44503485 ATATTAATAT
1 ATTTTAATAT
44503495 AATTGAACCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAATATTAAATA
Found at i:44509045 original size:18 final size:18
Alignment explanation
Indices: 44509024--44509060 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44509014 TTAATTTTTG
* *
44509024 AATTCGAATAACTCGAAT
1 AATTCAAATAAATCGAAT
44509042 AATTCAAATAAATCGAAT
1 AATTCAAATAAATCGAAT
44509060 A
1 A
44509061 CCAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCAAATAAATCGAAT
Found at i:44509608 original size:18 final size:18
Alignment explanation
Indices: 44509571--44509608 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
44509561 TAAAAAATCA
*
44509571 ATTTTTTATATTTAATAT
1 ATTTTTTATATTTAAAAT
44509589 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTATATTT-AAAAT
44509607 AT
1 AT
44509609 ATAGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTATATTTAAAAT
Found at i:44510183 original size:85 final size:85
Alignment explanation
Indices: 44510040--44510210 Score: 324
Period size: 85 Copynumber: 2.0 Consensus size: 85
44510030 AAGAAAGGTT
*
44510040 AGTACTTTTCTTTTCAAACCAAGTCATGCCCTTATTGCAATCATTCTCTACGTGTCCTTTCTTGC
1 AGTACTTTTCTTTTCAAACCAAGTCATGCCCTTATTGCAATCATTCTCTACATGTCCTTTCTTGC
*
44510105 CACAGAAATAACATTTGGCA
66 CACAGAAATAACACTTGGCA
44510125 AGTACTTTTCTTTTCAAACCAAGTCATGCCCTTATTGCAATCATTCTCTACATGTCCTTTCTTGC
1 AGTACTTTTCTTTTCAAACCAAGTCATGCCCTTATTGCAATCATTCTCTACATGTCCTTTCTTGC
44510190 CACAGAAATAACACTTGGCA
66 CACAGAAATAACACTTGGCA
44510210 A
1 A
44510211 TAAACTTTGC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (85 bp):
AGTACTTTTCTTTTCAAACCAAGTCATGCCCTTATTGCAATCATTCTCTACATGTCCTTTCTTGC
CACAGAAATAACACTTGGCA
Found at i:44523736 original size:16 final size:16
Alignment explanation
Indices: 44523693--44523739 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
44523683 TTTATATTTC
44523693 CATCTTTCT-ATTTTT
1 CATCTTTCTAATTTTT
*
44523708 CTACCTCTT-TAATTTTT
1 C-ATCT-TTCTAATTTTT
44523725 CATCTTTCTAATTTT
1 CATCTTTCTAATTTT
44523740 CTTTCCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 3 0.12
16 14 0.54
17 9 0.35
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (16 bp):
CATCTTTCTAATTTTT
Found at i:44525557 original size:46 final size:46
Alignment explanation
Indices: 44525490--44525581 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
44525480 AAGATAAAAG
* *
44525490 GTACACTATTGCACTCTCTATTTCTAAGTATTTGAGCATTCAATAA
1 GTACACTATCGAACTCTCTATTTCTAAGTATTTGAGCATTCAATAA
44525536 GTACACTATCGAACTCTCTATTTCTAAGTATTTGAGCATTCAATAA
1 GTACACTATCGAACTCTCTATTTCTAAGTATTTGAGCATTCAATAA
44525582 CAAACTTGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (46 bp):
GTACACTATCGAACTCTCTATTTCTAAGTATTTGAGCATTCAATAA
Found at i:44533103 original size:5 final size:6
Alignment explanation
Indices: 44533078--44533110 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
44533068 AAAGAATGGA
*
44533078 TTTATT TTTATT TTTGTT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTT
44533111 TCAAAGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:44533876 original size:23 final size:22
Alignment explanation
Indices: 44533850--44533903 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
44533840 CTTGTTTTAC
44533850 TATTTAAATAATAACAATAATAA
1 TATTTAAATAAT-ACAATAATAA
***
44533873 TATTTAAAATAATGTTATAATAA
1 TATTT-AAATAATACAATAATAA
44533896 TATTTAAA
1 TATTTAAA
44533904 ACTCGACCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TATTTAAATAATACAATAATAA
Found at i:44534498 original size:23 final size:23
Alignment explanation
Indices: 44534472--44534516 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
44534462 TATATTAAAT
* *
44534472 ATATATATATATTATTTTTAATC
1 ATATATACATATTACTTTTAATC
* *
44534495 ATATTTACATTTTACTTTTAAT
1 ATATATACATATTACTTTTAAT
44534517 TTTAATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATATACATATTACTTTTAATC
Found at i:44534635 original size:24 final size:26
Alignment explanation
Indices: 44534606--44534654 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
44534596 CTTGTTTTAA
*
44534606 TATTTG-TTT-TTATATTTTTAAATG
1 TATTTGATTTATTATATTTTAAAATG
44534630 TATTTGATTTATTATATTTTAAAAT
1 TATTTGATTTATTATATTTTAAAAT
44534655 TTTTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
TATTTGATTTATTATATTTTAAAATG
Found at i:44535022 original size:29 final size:29
Alignment explanation
Indices: 44534990--44535046 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
44534980 TTTTAGCTAA
* * *
44534990 ATTTGACCCTCAATTTTTTAAAAAGAGTC
1 ATTTGACCATCAATATTTCAAAAAGAGTC
44535019 ATTTGACCATCAATATTTCAAAAAGAGT
1 ATTTGACCATCAATATTTCAAAAAGAGT
44535047 TGAATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (29 bp):
ATTTGACCATCAATATTTCAAAAAGAGTC
Found at i:44536343 original size:18 final size:18
Alignment explanation
Indices: 44536320--44536356 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44536310 CGCATTAGGG
44536320 AATAACTAGGTGACATGC
1 AATAACTAGGTGACATGC
44536338 AATAACTAGGTGACATGC
1 AATAACTAGGTGACATGC
44536356 A
1 A
44536357 TATGACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (18 bp):
AATAACTAGGTGACATGC
Found at i:44537306 original size:28 final size:28
Alignment explanation
Indices: 44537223--44537318 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
44537213 ATGCATTGAT
** *
44537223 TTCATACATGCAGATTCATAGATACAAA
1 TTCATACATGTGGATTCATAGATACGAA
*
44537251 TTCATACATGTGGAATCATAGATACGAA
1 TTCATACATGTGGATTCATAGATACGAA
* *
44537279 TTCATACATGTGGATTCATATATGCGAA
1 TTCATACATGTGGATTCATAGATACGAA
* *
44537307 TTCGTGCATGTG
1 TTCATACATGTG
44537319 AACTCATTCT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (28 bp):
TTCATACATGTGGATTCATAGATACGAA
Found at i:44537309 original size:14 final size:14
Alignment explanation
Indices: 44537223--44537309 Score: 61
Period size: 14 Copynumber: 6.2 Consensus size: 14
44537213 ATGCATTGAT
44537223 TTCATACATGC-AGA
1 TTCATACATGCGA-A
* * *
44537237 TTCATAGATACAAA
1 TTCATACATGCGAA
*
44537251 TTCATACATGTGGAA
1 TTCATACATG-CGAA
* *
44537266 -TCATAGATACGAA
1 TTCATACATGCGAA
* *
44537279 TTCATACATGTGGA
1 TTCATACATGCGAA
*
44537293 TTCATATATGCGAA
1 TTCATACATGCGAA
44537307 TTC
1 TTC
44537310 GTGCATGTGA
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
13 3 0.06
14 48 0.89
15 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (14 bp):
TTCATACATGCGAA
Found at i:44537531 original size:84 final size:84
Alignment explanation
Indices: 44537414--44537567 Score: 245
Period size: 84 Copynumber: 1.8 Consensus size: 84
44537404 CAGACTTTTG
* *
44537414 CTTGAAAGATAGTCCATACAGACTCTTGCTTGAAAGATAGTTCATGTGGACTCATACTTGAAAGA
1 CTTGAAAGATAGTCCATACAGACTCCTACTTGAAAGATAGTTCATGTGGACTCATACTTGAAAGA
44537479 TAGTCCAAGCGAACTCCTA
66 TAGTCCAAGCGAACTCCTA
* ** * *
44537498 CTTGAAAGATAGTTCATATGGACTCCTATTTGAAAGATAGTTCATGTGGACTCCTACTTGAAAGA
1 CTTGAAAGATAGTCCATACAGACTCCTACTTGAAAGATAGTTCATGTGGACTCATACTTGAAAGA
44537563 TAGTC
66 TAGTC
44537568 GATGTGGACA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (84 bp):
CTTGAAAGATAGTCCATACAGACTCCTACTTGAAAGATAGTTCATGTGGACTCATACTTGAAAGA
TAGTCCAAGCGAACTCCTA
Found at i:44537572 original size:28 final size:28
Alignment explanation
Indices: 44537414--44537576 Score: 193
Period size: 28 Copynumber: 5.8 Consensus size: 28
44537404 CAGACTTTTG
* *** * *
44537414 CTTGAAAGATAGTCCATACAGACTCTTG
1 CTTGAAAGATAGTTCATGTGGACTCCTA
*
44537442 CTTGAAAGATAGTTCATGTGGACTCATA
1 CTTGAAAGATAGTTCATGTGGACTCCTA
* * * *
44537470 CTTGAAAGATAGTCCAAGCGAACTCCTA
1 CTTGAAAGATAGTTCATGTGGACTCCTA
*
44537498 CTTGAAAGATAGTTCATATGGACTCCTA
1 CTTGAAAGATAGTTCATGTGGACTCCTA
*
44537526 TTTGAAAGATAGTTCATGTGGACTCCTA
1 CTTGAAAGATAGTTCATGTGGACTCCTA
44537554 CTTGAAAGATAG-TCGATGTGGAC
1 CTTGAAAGATAGTTC-ATGTGGAC
44537577 ATTTGCTTCA
Statistics
Matches: 115, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 2 0.02
28 113 0.98
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (28 bp):
CTTGAAAGATAGTTCATGTGGACTCCTA
Found at i:44540207 original size:23 final size:23
Alignment explanation
Indices: 44540180--44540230 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
44540170 ATTTAAATAA
* *
44540180 TAAAATATTTTTATAATAATATT
1 TAAAATAGTGTTATAATAATATT
44540203 TAAAATAGTGTTATAATAATATT
1 TAAAATAGTGTTATAATAATATT
44540226 TAAAA
1 TAAAA
44540231 CTTGACCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TAAAATAGTGTTATAATAATATT
Found at i:44543289 original size:28 final size:28
Alignment explanation
Indices: 44543258--44543341 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
44543248 TCACAATTTT
* *
44543258 ATACGTGTAGATTTATAGATACAAATTC
1 ATACATGTAGATTCATAGATACAAATTC
* * ***
44543286 ATACATGTGGAATCATAGATATGGATTC
1 ATACATGTAGATTCATAGATACAAATTC
* *
44543314 ATACATGCAGATTCATAGATGCAAATTC
1 ATACATGTAGATTCATAGATACAAATTC
44543342 GTGCATGCGA
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (28 bp):
ATACATGTAGATTCATAGATACAAATTC
Found at i:44543483 original size:28 final size:28
Alignment explanation
Indices: 44543446--44543575 Score: 147
Period size: 28 Copynumber: 4.6 Consensus size: 28
44543436 CTGACTTTTG
* *
44543446 CTTGAAAGATAGTCCATGCAAACTCTTG
1 CTTGAAAGATAGTCCATGCGAACTCTTA
* * *
44543474 CTTGAAAGATAGTCCATGTGGACTCGTA
1 CTTGAAAGATAGTCCATGCGAACTCTTA
* *
44543502 CTTGAAAGATAGACCA-GACGGACTCTTA
1 CTTGAAAGATAGTCCATG-CGAACTCTTA
* *
44543530 CTTGAAAGATAGTTCATACGAACT-TCTA
1 CTTGAAAGATAGTCCATGCGAACTCT-TA
44543558 CTTGAAAGATAGTCCATG
1 CTTGAAAGATAGTCCATG
44543576 TGGATTTTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
27 2 0.02
28 83 0.98
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (28 bp):
CTTGAAAGATAGTCCATGCGAACTCTTA
Found at i:44551550 original size:14 final size:14
Alignment explanation
Indices: 44551533--44551559 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44551523 ATTACTTATA
44551533 GAAAATAATTTTTG
1 GAAAATAATTTTTG
44551547 GAAAATAATTTTT
1 GAAAATAATTTTT
44551560 TTTTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
GAAAATAATTTTTG
Found at i:44557707 original size:31 final size:30
Alignment explanation
Indices: 44557672--44557732 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
44557662 GAAACAGAAT
*
44557672 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
44557703 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
44557733 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:44562976 original size:26 final size:26
Alignment explanation
Indices: 44562945--44562994 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
44562935 GCTTCGTAAT
**
44562945 TTTTCAGGTTTTTTGGTTTCAACAGG
1 TTTTCAGGTTTTCAGGTTTCAACAGG
44562971 TTTTCAGGTTTTCAGGTTTCAACA
1 TTTTCAGGTTTTCAGGTTTCAACA
44562995 AGTGATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (26 bp):
TTTTCAGGTTTTCAGGTTTCAACAGG
Found at i:44567632 original size:46 final size:47
Alignment explanation
Indices: 44567526--44567647 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
44567516 TGTCTTCGAC
** * *
44567526 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
44567576 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
44567622 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
44567648 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:44572083 original size:35 final size:34
Alignment explanation
Indices: 44572044--44572127 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 34
44572034 TTTTCAAAAT
* *
44572044 TTTATATTGTTTATCTTAAACTCTTTTATACATTA
1 TTTATATTATTTAT-TTAAACTATTTTATACATTA
* * **
44572079 TTTATTTTATTT-TTTAAACTATTTTTTATTTTA
1 TTTATATTATTTATTTAAACTATTTTATACATTA
*
44572112 TGTATATTATTTATTT
1 TTTATATTATTTATTT
44572128 TAAATTTCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 26 0.65
34 4 0.10
35 10 0.25
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.65
Consensus pattern (34 bp):
TTTATATTATTTATTTAAACTATTTTATACATTA
Found at i:44572096 original size:33 final size:35
Alignment explanation
Indices: 44572044--44572157 Score: 88
Period size: 33 Copynumber: 3.3 Consensus size: 35
44572034 TTTTCAAAAT
* * * *
44572044 TTTATATTGTTTATCTTAAACTCTTTTATACATTA
1 TTTATTTTATTTATTTTAAACTCTTTTATAAATTA
* * **
44572079 TTTATTTTA-TT-TTTTAAACTATTTTTTATTTTA
1 TTTATTTTATTTATTTTAAACTCTTTTATAAATTA
* * * *
44572112 TGTATATTATTTATTTTAAATTTCTTCTTACAAATTA
1 TTTATTTTATTTATTTTAAA-CTCTT-TTATAAATTA
44572149 TTTATTTTA
1 TTTATTTTA
44572158 GACTTTCTAT
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
33 24 0.41
34 4 0.07
35 14 0.24
36 3 0.05
37 13 0.22
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (35 bp):
TTTATTTTATTTATTTTAAACTCTTTTATAAATTA
Found at i:44572244 original size:26 final size:25
Alignment explanation
Indices: 44572215--44572328 Score: 81
Period size: 26 Copynumber: 4.4 Consensus size: 25
44572205 TTGTGTTATT
44572215 TTATTTTAAATTATTTTGTATATTAA
1 TTATTTTAAATTATTTT-TATATTAA
* *
44572241 TTATTTTAAA-T-TGTTTATACT-A
1 TTATTTTAAATTATTTTTATATTAA
* * * * *
44572263 TTCACTCTAAATTGCTTTTTATAATAT
1 TT-ATTTTAAATT-ATTTTTATATTAA
44572290 TTATTTTAAACTTATTTTTTATGTATTAA
1 TTATTTTAAA-TTA-TTTTTA--TATTAA
44572319 TTATTTTAAA
1 TTATTTTAAA
44572329 ATTGTCTCAT
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.04
23 11 0.16
24 4 0.06
25 1 0.01
26 24 0.36
27 10 0.15
29 14 0.21
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (25 bp):
TTATTTTAAATTATTTTTATATTAA
Found at i:44572246 original size:46 final size:43
Alignment explanation
Indices: 44572171--44572258 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 43
44572161 TTTCTATATG
* *
44572171 TTATTTTAAATTGTTATATATTATTTATTTTAAGTTGTGTTATT
1 TTATTTTAAATTGTTATATATTAATTATTTTAAATTGT-TTATT
* *
44572215 TTATTTTAAATTATTTTGTATATTAATTATTTTAAATTGTTTAT
1 TTATTTTAAA-T-TGTTATATATTAATTATTTTAAATTGTTTAT
44572259 ACTATTCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 10 0.26
45 5 0.13
46 23 0.61
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (43 bp):
TTATTTTAAATTGTTATATATTAATTATTTTAAATTGTTTATT
Found at i:44572510 original size:16 final size:18
Alignment explanation
Indices: 44572465--44572510 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 18
44572455 CGTATTTTCT
44572465 TATTATTGTCATTCACTTG
1 TATTATTGTCATTCAC-TG
44572484 TATAATATTGT-ATTCA-TG
1 TAT--TATTGTCATTCACTG
44572502 TATTATTGT
1 TATTATTGT
44572511 TCCATGCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.24
18 5 0.20
19 3 0.12
20 5 0.20
21 6 0.24
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TATTATTGTCATTCACTG
Found at i:44577723 original size:378 final size:378
Alignment explanation
Indices: 44577019--44577776 Score: 1329
Period size: 378 Copynumber: 2.0 Consensus size: 378
44577009 CTTGCATAAG
*
44577019 AGTGTTGTATGTGACAGTATCCGGGATTGGTCCCTTTCGAGATATTTCATGAAAGAGTTCCATTG
1 AGTGCTGTATGTGACAGTATCCGGGATTGGTCCCTTTCGAGATATTTCATGAAAGAGTTCCATTG
* * *
44577084 CTTCGTCTAACCTTTTACCTTTGCAATATCCATTTATCATGGTGTTGTAAGTAACTATATCACGT
66 CTTCGTCTAACCTCTTACCTTTGCAATATCCATTGATCATGGTGCTGTAAGTAACTATATCACGT
* *
44577149 GCACAACCCTTCTCAATCATCAAGTTGAAAAGTCTTCTAGCTTTATCCATTTTGTTCTGCAAGCA
131 GCACAACCCTTCTCAATCATCAAGTTGAAAAGTCTTCCAGCTTTATCCATTTCGTTCTGCAAGCA
44577214 ATGGCCGTTGATTAATGCATTAAGGGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGA
196 ATGGCCGTTGATTAATGCATTAAGGGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGA
44577279 CAACGATATCCTCAGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACCAATGTACTATAC
261 CAACGATATCCTCAGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACCAATGTACTATAC
**
44577344 GTGACAACATTAGGTTCAATGCCTTGCTTTCTCATTGTGTCAACGGTCTCTAC
326 GTGACAACATTAGGTTCAATGCCTTGCTTTCTCATTGTGTCAACAATCTCTAC
* *
44577397 AGTGCTGTATGTGACAGTATTCGGGATTGGTCCCTTTTGAGATATTTCATGAAAGAGTTCCATTG
1 AGTGCTGTATGTGACAGTATCCGGGATTGGTCCCTTTCGAGATATTTCATGAAAGAGTTCCATTG
* * *
44577462 CTTCGTCTAACCTCTT-CGCTTTGTAATATCCATTGATCATGGTGCTGTAAGTAACTATATTAGG
66 CTTCGTCTAACCTCTTAC-CTTTGCAATATCCATTGATCATGGTGCTGTAAGTAACTATATCACG
44577526 TGCACAACCCTTCTCAATCATCAAGTTGAAAAGTCTTCCAGCTTTATCCATTTCGTTCTGCAAGC
130 TGCACAACCCTTCTCAATCATCAAGTTGAAAAGTCTTCCAGCTTTATCCATTTCGTTCTGCAAGC
*
44577591 AATGGCCGTTGATTAATGCATTATGGGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGCG
195 AATGGCCGTTGATTAATGCATTAAGGGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGCG
* * * *
44577656 TCAACGATATCCTCAGCTTCAGAGACCATCCCTTCCTTGCAATGTGCATCAACCAATTTATTATA
260 ACAACGATATCCTCAGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACCAATGTACTATA
*
44577721 CGTGGCAACATTAGGTTCAATGCCTTGCTTTCTCATTGTGTCAACAATCTCTAC
325 CGTGACAACATTAGGTTCAATGCCTTGCTTTCTCATTGTGTCAACAATCTCTAC
44577775 AG
1 AG
44577777 CTTTAGAAAT
Statistics
Matches: 360, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
377 1 0.00
378 359 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (378 bp):
AGTGCTGTATGTGACAGTATCCGGGATTGGTCCCTTTCGAGATATTTCATGAAAGAGTTCCATTG
CTTCGTCTAACCTCTTACCTTTGCAATATCCATTGATCATGGTGCTGTAAGTAACTATATCACGT
GCACAACCCTTCTCAATCATCAAGTTGAAAAGTCTTCCAGCTTTATCCATTTCGTTCTGCAAGCA
ATGGCCGTTGATTAATGCATTAAGGGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGA
CAACGATATCCTCAGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACCAATGTACTATAC
GTGACAACATTAGGTTCAATGCCTTGCTTTCTCATTGTGTCAACAATCTCTAC
Found at i:44577733 original size:105 final size:105
Alignment explanation
Indices: 44577621--44577825 Score: 270
Period size: 105 Copynumber: 2.0 Consensus size: 105
44577611 TTATGGGTAA
*
44577621 CAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAACGATATC-CT-CAGCTTCAGAGACCA
1 CAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAAC-A-ATCTCTACAGCTTCAGAAACCA
* *
44577684 TCCCTTCCTTGCAATGTGCATCAACCAATTTATTATACGTGG
64 TCCCTTCCTTGCAAAGTGCATCAACCAATATATTATACGTGG
* * * * * * * *
44577726 CAACATTAGGTTCAATGCCTTGCTTTCTCATTGTGTCAACAATCTCTACAGCTTTAGAAATCGTT
1 CAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATCTCTACAGCTTCAGAAACCATC
*
44577791 CCTTCCTTGCAAAGTGCATCAATCAATATATTATA
66 CCTTCCTTGCAAAGTGCATCAACCAATATATTATA
44577826 TGTAACAATA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
103 3 0.03
104 3 0.03
105 80 0.93
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (105 bp):
CAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATCTCTACAGCTTCAGAAACCATC
CCTTCCTTGCAAAGTGCATCAACCAATATATTATACGTGG
Found at i:44580430 original size:21 final size:21
Alignment explanation
Indices: 44580381--44580438 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
44580371 GGTATAAGCC
44580381 TATAT-TGATAATTCAACAATG
1 TATATATG-TAATTCAACAATG
* *
44580402 TATGTATGTAATTGAA-AATG
1 TATATATGTAATTCAACAATG
44580422 TTATATATG-AATT-AACA
1 -TATATATGTAATTCAACA
44580439 TTTGGTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 9 0.29
21 18 0.58
22 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (21 bp):
TATATATGTAATTCAACAATG
Found at i:44585865 original size:23 final size:23
Alignment explanation
Indices: 44585783--44585869 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
44585773 CCTGATCAGT
*
44585783 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
44585805 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
44585825 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
44585848 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
44585870 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:44587534 original size:16 final size:17
Alignment explanation
Indices: 44587499--44587534 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
44587489 CCTAATTCTC
44587499 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
44587515 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
44587530 CCTTC
1 CCTTC
44587535 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:44590208 original size:25 final size:26
Alignment explanation
Indices: 44590180--44590248 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
44590170 ACCGGTTTGT
44590180 AGCTCGTGA-GAGCTTACCGATACTC
1 AGCTCGTGATGAGCTTACCGATACTC
* *
44590205 AGCTCAT-ATGAGCTTACCGATATTC
1 AGCTCGTGATGAGCTTACCGATACTC
44590230 AGCTCG-GATGAGCTTACCG
1 AGCTCGTGATGAGCTTACCG
44590249 TTTATCGCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (26 bp):
AGCTCGTGATGAGCTTACCGATACTC
Found at i:44590234 original size:50 final size:50
Alignment explanation
Indices: 44590154--44590248 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
44590144 GGACTCACCA
* * *
44590154 CAGCTCTTATGAGCTTACCGGTTTGTAGCTCGTGA-GAGCTTACCGATACT
1 CAGCTCATATGAGCTTACCGATTTGCAGCTCG-GATGAGCTTACCGATACT
44590204 CAGCTCATATGAGCTTACCGATATT-CAGCTCGGATGAGCTTACCG
1 CAGCTCATATGAGCTTACCGAT-TTGCAGCTCGGATGAGCTTACCG
44590249 TTTATCGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
49 2 0.05
50 36 0.90
51 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (50 bp):
CAGCTCATATGAGCTTACCGATTTGCAGCTCGGATGAGCTTACCGATACT
Found at i:44590264 original size:24 final size:25
Alignment explanation
Indices: 44590189--44590266 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
44590179 TAGCTCGTGA
* **
44590189 GAGCTTACCGATACTCAGCTCATAT
1 GAGCTTACCGATATTCAGCTCGCAT
*
44590214 GAGCTTACCGATATTCAGCTCGGAT
1 GAGCTTACCGATATTCAGCTCGCAT
*
44590239 GAGCTTACCG-TTTATC-GCTCGCAT
1 GAGCTTACCGATAT-TCAGCTCGCAT
44590263 GAGC
1 GAGC
44590267 ATACATGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
24 13 0.28
25 34 0.72
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (25 bp):
GAGCTTACCGATATTCAGCTCGCAT
Found at i:44592546 original size:21 final size:20
Alignment explanation
Indices: 44592496--44592553 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
44592486 ATAATAAGAT
44592496 AATGAAAATGAGAATAAAAAA
1 AATGAAAATGA-AATAAAAAA
* * *
44592517 AATAAAAATGAAATAAATAC
1 AATGAAAATGAAATAAAAAA
44592537 AATGATAAATGAAATAA
1 AATGA-AAATGAAATAA
44592554 CAAAGAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (20 bp):
AATGAAAATGAAATAAAAAA
Found at i:44592961 original size:3 final size:3
Alignment explanation
Indices: 44592955--44593088 Score: 87
Period size: 3 Copynumber: 45.3 Consensus size: 3
44592945 TAATAAAAGC
* * * * *
44592955 AAT AAT AAT ACT AA- ATAT AAC AAT AGT AAT ATT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * * *
44593000 AAT AGC AAT AAA AAT AAA AAT AAT AAC AAT GAT AAT AA- AA- AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
44593046 AGT AAT AAT AAT AAT AAT GAA- AAT AAG AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
44593089 CATTAAATTA
Statistics
Matches: 97, Mismatches: 29, Indels: 10
0.71 0.21 0.07
Matches are distributed among these distances:
2 7 0.07
3 87 0.90
4 3 0.03
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:44592978 original size:21 final size:21
Alignment explanation
Indices: 44592946--44593138 Score: 63
Period size: 21 Copynumber: 9.3 Consensus size: 21
44592936 TAGTAGTTAT
44592946 AATAA-AAGCAATAATAATACTA
1 AATAATAA-CAATAATAATA-TA
* *
44592968 AAT-ATAACAATAGTAATATT
1 AATAATAACAATAATAATATA
*
44592988 AATAATAAAAATAATAGCA-ATA
1 AATAATAACAATAATA--ATATA
* *
44593010 AA-AATAAAAATAATAACA-A
1 AATAATAACAATAATAATATA
* *
44593029 TGATAATAA-AA-AATACTAGT-
1 -AATAATAACAATAATAATA-TA
* *
44593049 AATAATAATAATAATGAAAATA
1 AATAATAACAATAAT-AATATA
*
44593071 AGAGTAATAATAATAATACAT-TA
1 A-A-TAATAACAATAATA-ATATA
*
44593094 AAT--T-ACAATAGTAA-AGT-
1 AATAATAACAATAATAATA-TA
* * *
44593111 AATAATAATAGTGATAATATA
1 AATAATAACAATAATAATATA
44593132 AATAATA
1 AATAATA
44593139 TATGTATGAA
Statistics
Matches: 130, Mismatches: 18, Indels: 47
0.67 0.09 0.24
Matches are distributed among these distances:
17 4 0.03
18 8 0.06
19 16 0.12
20 17 0.13
21 52 0.40
22 13 0.10
23 6 0.05
24 14 0.11
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (21 bp):
AATAATAACAATAATAATATA
Found at i:44593188 original size:3 final size:3
Alignment explanation
Indices: 44593180--44593222 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
44593170 ATGTATATAT
*
44593180 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GA-A ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A
44593223 AAATGGCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:44594749 original size:21 final size:20
Alignment explanation
Indices: 44594697--44594749 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
44594687 CGGCTTGTAG
44594697 CACGGGCGTGTCCCTTAGTCA
1 CACGGGCGTGTCCCTTA-TCA
* *
44594718 CACAGGTGTGTCCCCTT-TCCA
1 CACGGGCGTGT-CCCTTAT-CA
44594739 CACGGGCGTGT
1 CACGGGCGTGT
44594750 GACTCCTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 20 0.77
22 5 0.19
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.25
Consensus pattern (20 bp):
CACGGGCGTGTCCCTTATCA
Found at i:44597997 original size:105 final size:105
Alignment explanation
Indices: 44597866--44598079 Score: 259
Period size: 105 Copynumber: 2.0 Consensus size: 105
44597856 ATTATGGGTA
*
44597866 ACAACATTAGGCTCAATGCCTCGCTTTATAATTGCGTCAACAATATCCT-CAGCTTCAGAGACCA
1 ACAACATTAGGCTCAATGCCTCGCTTTATAATTGCGTCAACAATAT-CTACAGCTTCAGAAACCA
* *
44597930 TCCCTTCCTTGCAATGCGCATCAACCAATGTATTATACGTG
65 TCCCTTCCTTGCAAAGCGCATCAACCAATATATTATACGTG
* * * * * * * * * *
44597971 ACAACATTAGGTTCAATGCCTTGCTTTCTCATTGTGTCAACGATCTCTACAGCTTTAGAAATCGT
1 ACAACATTAGGCTCAATGCCTCGCTTTATAATTGCGTCAACAATATCTACAGCTTCAGAAACCAT
* * * *
44598036 TCCTTCCTTGCAAAGTGCATCAATCAATATATTATATGTG
66 CCCTTCCTTGCAAAGCGCATCAACCAATATATTATACGTG
44598076 ACAA
1 ACAA
44598080 TATCAAGTGA
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 2 0.02
105 89 0.98
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (105 bp):
ACAACATTAGGCTCAATGCCTCGCTTTATAATTGCGTCAACAATATCTACAGCTTCAGAAACCAT
CCCTTCCTTGCAAAGCGCATCAACCAATATATTATACGTG
Done.