Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015283.1 Kokia drynarioides strain JFW-HI SEQ_130328, whole genome shotgun sequence
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: 430064
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 639 characters in sequence are not A, C, G, or T
Found at i:1950 original size:2 final size:2
Alignment explanation
Indices: 1945--1970 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1935 AAATAATAAA
1945 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1971 GTGTAAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5285 original size:31 final size:30
Alignment explanation
Indices: 5247--5307 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
5237 AATTAGTAAA
5247 AATAAAATTAT-ACATTAATCTCTTTAAAAAT
1 AATAAAATTATGA-ATTAATCT-TTTAAAAAT
* *
5278 AATAAAATTTTGATTTAATCTTTTAAAAAT
1 AATAAAATTATGAATTAATCTTTTAAAAAT
5308 TATATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 17 0.63
32 1 0.04
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (30 bp):
AATAAAATTATGAATTAATCTTTTAAAAAT
Found at i:5795 original size:20 final size:19
Alignment explanation
Indices: 5749--5801 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
5739 ATTAAAAATA
* * *
5749 TATATTTTTTAATTATTTT
1 TATATTTTTTAAATAATGT
5768 TA-ATTTTTCTAAATAATGT
1 TATATTTTT-TAAATAATGT
5787 TATATTTTTTTAAAT
1 TATA-TTTTTTAAAT
5802 TTCTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 11 0.39
20 6 0.21
21 5 0.18
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TATATTTTTTAAATAATGT
Found at i:6588 original size:27 final size:29
Alignment explanation
Indices: 6558--6619 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
6548 CTTCGAAATT
*
6558 TTTTATT-TTTTTC-CAAAACTTTTACTC
1 TTTTATTACTTTTCACAAAACTTTTACTC
* *
6585 TTTT-TTACTTTTCATTAAAACTTTTACTT
1 TTTTATTACTTTTCA-CAAAACTTTTACTC
6614 TTTTAT
1 TTTTAT
6620 CATCCAACCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 2 0.07
27 9 0.32
29 16 0.57
30 1 0.04
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTATTACTTTTCACAAAACTTTTACTC
Found at i:6730 original size:25 final size:25
Alignment explanation
Indices: 6701--6748 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
6691 TTACTTTCCC
*
6701 TATTTATTTTCTCTCCAAATTTTCT
1 TATTTATTTTCTCTCAAAATTTTCT
6726 TATTTATTTTCTCTCAAAATTTT
1 TATTTATTTTCTCTCAAAATTTT
6749 ACTTCCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTTATTTTCTCTCAAAATTTTCT
Found at i:7562 original size:14 final size:14
Alignment explanation
Indices: 7543--7580 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
7533 GTTAATATAC
7543 TCAAATTTTAAATT
1 TCAAATTTTAAATT
*
7557 TCAAATTTCAAATT
1 TCAAATTTTAAATT
7571 T-AAATTTTAA
1 TCAAATTTTAA
7581 CATAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
TCAAATTTTAAATT
Found at i:7577 original size:6 final size:7
Alignment explanation
Indices: 7543--7577 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
7533 GTTAATATAC
7543 TCAAATT
1 TCAAATT
*
7550 TTAAATT
1 TCAAATT
7557 TCAAATT
1 TCAAATT
7564 TCAAATT
1 TCAAATT
7571 T-AAATT
1 TCAAATT
7577 T
1 T
7578 TAACATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (7 bp):
TCAAATT
Found at i:7796 original size:107 final size:107
Alignment explanation
Indices: 7678--7895 Score: 355
Period size: 107 Copynumber: 2.0 Consensus size: 107
7668 ACACAACTTT
* * * *
7678 TTACTTCTTTTTGAGATTATTAATAATGGTCAGATTTTAGTTTTGGTTCTTATATTATGCTCAAA
1 TTACTTCTTTTTGAGATTATTAATAATGGTCAAATTTTAATTTTGATTCTTATATTATACTCAAA
* *
7743 TTTAAAATTTAGTCTTTATATTTTAATTTTTTATATAATCAA
66 TTTAAAATTTAATCTTTATATTTTAATTTTTTACATAATCAA
* * *
7785 TTACTTTTTTTTTAGATTATTAATAATGGTCAAATTTTAATTTTGATTCTTATATTATACTCAAT
1 TTACTTCTTTTTGAGATTATTAATAATGGTCAAATTTTAATTTTGATTCTTATATTATACTCAAA
7850 TTTAAAATTTAATCTTTATATTTTAATTTTTTACATAATCAA
66 TTTAAAATTTAATCTTTATATTTTAATTTTTTACATAATCAA
7892 TTAC
1 TTAC
7896 CTCAACTTTT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 102 1.00
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (107 bp):
TTACTTCTTTTTGAGATTATTAATAATGGTCAAATTTTAATTTTGATTCTTATATTATACTCAAA
TTTAAAATTTAATCTTTATATTTTAATTTTTTACATAATCAA
Found at i:11511 original size:2 final size:2
Alignment explanation
Indices: 11506--11541 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11496 TATAAAAATA
11506 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
11542 TTTTGGACAA
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:21446 original size:21 final size:21
Alignment explanation
Indices: 21422--21467 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21412 AAAATTATTG
21422 AAAAATAAAATAAAAAA-CT-TC
1 AAAAA-AAAA-AAAAAACCTCTC
21443 AAAAAAAAAAAAAAACCTCTC
1 AAAAAAAAAAAAAAACCTCTC
21464 AAAA
1 AAAA
21468 TTAAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (21 bp):
AAAAAAAAAAAAAAACCTCTC
Found at i:34940 original size:30 final size:30
Alignment explanation
Indices: 34906--34966 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
34896 CATAATGTTT
34906 TTTAAGGTAAATACACATATAACTGTTCTA
1 TTTAAGGTAAATACACATATAACTGTTCTA
34936 TTTAAGGTAAATACACATATAACTGTTCTA
1 TTTAAGGTAAATACACATATAACTGTTCTA
34966 T
1 T
34967 CTTGACAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (30 bp):
TTTAAGGTAAATACACATATAACTGTTCTA
Found at i:35666 original size:24 final size:24
Alignment explanation
Indices: 35619--35677 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
35609 TAAAGTAGGT
*
35619 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATTA
35642 TATATTATAATTTTTACTAAT-TTA
1 TATATTATAATTTTT-CTAATATTA
*
35666 TATTTTAATAAT
1 TATATT-ATAAT
35678 AATTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 17 0.55
25 10 0.32
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATTA
Found at i:35688 original size:15 final size:14
Alignment explanation
Indices: 35669--35755 Score: 52
Period size: 14 Copynumber: 6.0 Consensus size: 14
35659 TAATTTATAT
35669 TTTAATAATAATTA
1 TTTAATAATAATTA
* *
35683 TATTAAAAAT-GTTA
1 T-TTAATAATAATTA
* *
35697 TTAAATTAATTATTA
1 TTTAA-TAATAATTA
* *
35712 TTTTATTAA-ATTGTA
1 -TTTAATAATAAT-TA
35727 TTTAATAATAATTA
1 TTTAATAATAATTA
*
35741 TTTAAAATATAATTA
1 TTTAATA-ATAATTA
35756 AATTATTTGT
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
13 3 0.06
14 24 0.44
15 24 0.44
16 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:35706 original size:29 final size:27
Alignment explanation
Indices: 35674--35760 Score: 70
Period size: 29 Copynumber: 3.1 Consensus size: 27
35664 TATATTTTAA
35674 TAATAATTATATTAAAAATGTTATTAAAT
1 TAATAATTAT-TTAAAAAT-TTATTAAAT
* * *
35703 TAATTATTATTTTATTAAATTGTATTTAA-
1 TAATAATTA-TTTA-AAAATT-TATTAAAT
*
35732 TAATAATTATTT-AAAATATAATTAAAT
1 TAATAATTATTTAAAAAT-TTATTAAAT
35759 TA
1 TA
35761 TTTGTTATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
26 9 0.20
27 3 0.07
28 3 0.07
29 20 0.43
30 11 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
TAATAATTATTTAAAAATTTATTAAAT
Found at i:35731 original size:26 final size:25
Alignment explanation
Indices: 35702--35809 Score: 63
Period size: 26 Copynumber: 4.0 Consensus size: 25
35692 TGTTATTAAA
35702 TTAATTATTATTTTATTAAATTGTAT
1 TTAATTATTATTTTATTAAATT-TAT
* * * *
35728 TTAATAATAATTATTTAAAATATAATTAAA
1 TTAAT--T-ATTATTT-TATTA-AATTTAT
* *
35758 TTATTTGTTATTTTTATTAAATTATAT
1 TTAATTATTA-TTTTATTAAATT-TAT
* *
35785 TTAATAATAATTTTATTAAAATTTA
1 TTAATTATTATTTTATT-AAATTTA
35810 ATAACAAGAA
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
26 18 0.30
27 18 0.30
28 5 0.08
29 7 0.12
30 8 0.13
31 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAATTATTATTTTATTAAATTTAT
Found at i:36926 original size:62 final size:63
Alignment explanation
Indices: 36810--36931 Score: 210
Period size: 63 Copynumber: 2.0 Consensus size: 63
36800 CATATCATTA
*
36810 TCTCAATATCATTTTACAACAGTTAATCGACATGAAACACATAATTTTAGATACTCTCATTTT
1 TCTCAATATCATTTTACAACAGTTAATCAACATGAAACACATAATTTTAGATACTCTCATTTT
* *
36873 TCTCAATATCATTTTACAACATTTAATCAACATG-AACATATAATTTTAGATACTCTCAT
1 TCTCAATATCATTTTACAACAGTTAATCAACATGAAACACATAATTTTAGATACTCTCAT
36932 CAAAATACCA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 24 0.43
63 32 0.57
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39
Consensus pattern (63 bp):
TCTCAATATCATTTTACAACAGTTAATCAACATGAAACACATAATTTTAGATACTCTCATTTT
Found at i:37328 original size:168 final size:168
Alignment explanation
Indices: 37050--37383 Score: 605
Period size: 168 Copynumber: 2.0 Consensus size: 168
37040 TGTTTTATAT
37050 TTTTTTCACCCAATGGTTACACCATAATCTAGTTAAAGTAAACATTTTGTATAATATTTTTATAT
1 TTTTTTCACCCAATGGTTACACCATAATCTAGTTAAAGTAAACATTTTGTATAATATTTTTATAT
37115 AATTTTTTTGAAATTTTGTTTTTAAAATAAGCTTTCAAATTTTATATTTGAAATTTTCTTTGTTT
66 AATTTTTTTGAAATTTTGTTTTTAAAATAAGCTTTCAAATTTTATATTTGAAATTTTCTTTGTTT
* *
37180 TTTTAAACTTATTTTTTATTTGGCTGTCATTCACCATA
131 TTTTAAACATATTTTTTAATTGGCTGTCATTCACCATA
* * *
37218 TTTTTTCACGCAATGGTTACACCTTAATCTAGTTAAAGTAAACATTTTGTATAATATTTTTCTAT
1 TTTTTTCACCCAATGGTTACACCATAATCTAGTTAAAGTAAACATTTTGTATAATATTTTTATAT
* *
37283 ACTTTTTTTGAAATTTTGTTTTTAGAATAAGCTTTCAAATTTTATATTTGAAATTTTCTTTGTTT
66 AATTTTTTTGAAATTTTGTTTTTAAAATAAGCTTTCAAATTTTATATTTGAAATTTTCTTTGTTT
37348 TTTTAAACATATTTTTTAATTGGCTGTCATTCACCA
131 TTTTAAACATATTTTTTAATTGGCTGTCATTCACCA
37384 AATCATCAAC
Statistics
Matches: 159, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 159 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.51
Consensus pattern (168 bp):
TTTTTTCACCCAATGGTTACACCATAATCTAGTTAAAGTAAACATTTTGTATAATATTTTTATAT
AATTTTTTTGAAATTTTGTTTTTAAAATAAGCTTTCAAATTTTATATTTGAAATTTTCTTTGTTT
TTTTAAACATATTTTTTAATTGGCTGTCATTCACCATA
Found at i:52316 original size:23 final size:23
Alignment explanation
Indices: 52265--52309 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
52255 ATAAAATTAT
52265 TAAATA-TTAAAATAAAATAAAA
1 TAAATATTTAAAATAAAATAAAA
52287 TAAATATTTAAAA-AAAATTAAAA
1 TAAATATTTAAAATAAAA-TAAAA
52310 ATAATATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAATATTTAAAATAAAATAAAA
Found at i:54228 original size:16 final size:16
Alignment explanation
Indices: 54209--54242 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54199 AGCTTACATT
* *
54209 GTCTTGTGCTTGCAAG
1 GTCTTGGGCTCGCAAG
54225 GTCTTGGGCTCGCAAG
1 GTCTTGGGCTCGCAAG
54241 GT
1 GT
54243 GTCACCTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.21, G:0.35, T:0.32
Consensus pattern (16 bp):
GTCTTGGGCTCGCAAG
Found at i:68180 original size:51 final size:50
Alignment explanation
Indices: 68124--68223 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 50
68114 AATTACTTTC
*
68124 ACTGGGTTTTATAAAAAGAAAAAACTGACACTAATCCCTTTAGATTTACTT
1 ACTGGGTTTTATAAAAAGAAAAAACTAACACTAATCCCTTT-GATTTACTT
*
68175 ACTGGGTTTTATAAAAAGAAAAAACTAACACTAATCCCTTTTATTTACT
1 ACTGGGTTTTATAAAAAGAAAAAACTAACACTAATCCCTTTGATTTACT
68224 GGGTTTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 7 0.15
51 40 0.85
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (50 bp):
ACTGGGTTTTATAAAAAGAAAAAACTAACACTAATCCCTTTGATTTACTT
Found at i:71623 original size:22 final size:23
Alignment explanation
Indices: 71595--71654 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
71585 GCATTAATAA
*
71595 TAATAATAATAAATAATTGTT-T
1 TAATAATAATAAATAATTATTAT
*
71617 TAATAATAATAATATTATTATTAT
1 TAATAATAATAA-ATAATTATTAT
71641 TAATTAATAATAAA
1 TAA-TAATAATAAA
71655 AAAAGAAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 12 0.36
23 7 0.21
24 5 0.15
25 9 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATAATAATAAATAATTATTAT
Found at i:71647 original size:28 final size:27
Alignment explanation
Indices: 71587--71653 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 27
71577 TGCTGATAGC
71587 ATTAA-TAATAATAATAATAAATAATT
1 ATTAATTAATAATAATAATAAATAATT
* * *
71613 GTT--TTAATAATAATAATATTATTATT
1 ATTAATTAATAATAATAATA-AATAATT
71639 ATTAATTAATAATAA
1 ATTAATTAATAATAA
71654 AAAAAGAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 14 0.42
26 9 0.27
28 10 0.30
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
ATTAATTAATAATAATAATAAATAATT
Found at i:71883 original size:17 final size:19
Alignment explanation
Indices: 71861--71895 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
71851 CTTTTTTTAA
71861 AAAAAAGA-AAGA-AGAAT
1 AAAAAAGAGAAGAGAGAAT
71878 AAAAAAGAGAAGAGAGAA
1 AAAAAAGAGAAGAGAGAA
71896 AACCTAGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (19 bp):
AAAAAAGAGAAGAGAGAAT
Found at i:72681 original size:59 final size:59
Alignment explanation
Indices: 72589--72909 Score: 266
Period size: 59 Copynumber: 5.4 Consensus size: 59
72579 GAGGTCCTTA
* *
72589 AACTTCCAAAAATTTCATTTTT-ACCCCTG-AACTTCCAAAAATCCTACTTTTAACCTCGT
1 AACTTCCAAAAATTCCATTTTTGA-CCCTGAAACTTCCAAAAATCC-ATTTTTAACCTCGT
** **
72648 AACTTCCAAAAATTCCATTTTT-ACTGTTG-AACTTCCAAAAATCTCATTTTTAACC-CAAA
1 AACTTCCAAAAATTCCATTTTTGAC-CCTGAAACTTCCAAAAATC-CATTTTTAACCTC-GT
** * * * *
72707 AACTTAAAAAAATTCCATTTTTGACCTTGAAACTTTCAAAATTTCCATTTTTACCCTCGT
1 AACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCCAAAA-ATCCATTTTTAACCTCGT
* * * *
72767 -GCTTTCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG-
1 AACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCCAAAAA-TCCATTTTTAACCTCGT
* * * ** **
72825 AACTTCCAAAAATCCCGTTTTTGATCCC-GAAACATCCAAAAATTCTGTTTTTTCCCTCG-
1 AACTTCCAAAAATTCCATTTTTGA-CCCTGAAACTTCCAAAAA-TCCATTTTTAACCTCGT
*
72884 AACTTCC-AAAATCTCCATTTTCGACC
1 AACTTCCAAAAAT-TCCATTTTTGACC
72910 TCAAAACTCT
Statistics
Matches: 219, Mismatches: 32, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
58 9 0.04
59 181 0.83
60 26 0.12
61 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTGACCCTGAAACTTCCAAAAATCCATTTTTAACCTCGT
Found at i:72845 original size:29 final size:29
Alignment explanation
Indices: 72589--72904 Score: 259
Period size: 30 Copynumber: 10.7 Consensus size: 29
72579 GAGGTCCTTA
*
72589 AACTTCCAAAAATTTCATTTTTACCC-CTG
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* *
72618 AACTTCCAAAAA-TCCTACTTTTAACCTCG
1 AACTTCCAAAAATTCC-ATTTTTACCCTCG
** *
72647 TAACTTCCAAAAATTCCATTTTTACTGTTG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
***
72677 AACTTCCAAAAA-TCTCATTTTTAACCCAAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCTCG
** *
72707 AACTTAAAAAAATTCCATTTTTGA-CCTTG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
72736 AAACTTTCAAAATTTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
** *
72766 TGCTTTCAAAAATTCCATTTTTGACCC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
72795 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
72825 AACTTCCAAAAATCCCGTTTTTGATCC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* ** *
72854 AAACATCCAAAAATTCTGTTTTTTCCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
72884 AACTTCC-AAAATCTCCATTTT
1 AACTTCCAAAAAT-TCCATTTT
72905 CGACCTCAAA
Statistics
Matches: 231, Mismatches: 40, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
28 9 0.04
29 104 0.45
30 113 0.49
31 5 0.02
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:73481 original size:18 final size:18
Alignment explanation
Indices: 73458--73495 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
73448 TTTTACAAAG
73458 GAAGGCTCGTTATTTCTA
1 GAAGGCTCGTTATTTCTA
73476 GAAGGCTCGTTATTTCTA
1 GAAGGCTCGTTATTTCTA
73494 GA
1 GA
73496 TCTTGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (18 bp):
GAAGGCTCGTTATTTCTA
Found at i:84977 original size:205 final size:205
Alignment explanation
Indices: 84620--85431 Score: 1196
Period size: 205 Copynumber: 4.0 Consensus size: 205
84610 GTGACCATCC
*
84620 ACAAACGACGCGGTCATCTTTCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * *
84685 TGTGAGTAAATCTTCGAATCTCAGCTTCTTGATAAGACACCGAGAAGTAGATCGAAGCAATAAAC
66 TGTGAGTAAATCTTCGAATCCCAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
* * * * * *
84750 GGTTAGCTTCCTGATAAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAA
131 GGTGAGCTTCCTGATGAGATACTAAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
*
84815 GCGAATTGAA
196 GCAAATTGAA
* * *
84825 ATAAACGACGCGATCATCTTTCTGATGAGATACTGAGAAAAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * * *
84890 TGTGAGTAAACCTTCGAACCCCAGCTT-TCTAATGAGACACCGAGAAGTAGGTCGAAACAATAAA
66 TGTGAGTAAATCTTCGAATCCCAGCTTCT-TGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA
84954 CGGTGAGCTTCCTGATGAGATACTAAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
130 CGGTGAGCTTCCTGATGAGATACTAAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
85019 AGCAAATTGAA
195 AGCAAATTGAA
* ** * *
85030 ACAAATGACATGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACGACGCGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * * *
85095 TATGAGAAAATCTTCGAATCCCAGTTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAC
66 TGTGAGTAAATCTTCGAATCCCAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
*
85160 GGTGAGCTTCCTGATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
131 GGTGAGCTTCCTGATGAGATACTAAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
85225 GCAAATTGAA
196 GCAAATTGAA
* * * *
85235 ACAAATGACGTGGTCATC-TTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACTCATGCTCG
1 ACAAACGACGCGGTCATCTTTC-TGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCG
* * * *
85299 ATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATGAGACACTGTGAAGCAGGTCGAAGTAATAAA
65 ATGTGAGTAAATCTTCGAATCCCAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA
* * * * *
85364 TGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGA
130 CGGTGAGCTTCCTGATGAGATACTAAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
85429 AGC
195 AGC
85432 GAACCAAATT
Statistics
Matches: 552, Mismatches: 52, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
204 3 0.01
205 549 0.99
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (205 bp):
ACAAACGACGCGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGTAAATCTTCGAATCCCAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
GGTGAGCTTCCTGATGAGATACTAAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
GCAAATTGAA
Found at i:85412 original size:37 final size:38
Alignment explanation
Indices: 85371--85468 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 38
85361 AAATGGTTAG
* *
85371 CTTCCTGATGAGATACTA-AGAAGTGGACCAAATTCGT
1 CTTCCTGATGAGATACTAGAGAAGCGAACCAAATTCGT
*
85408 CTTCCTGATAAGATAC-AGAGAAGCGAACCAAATTCGT
1 CTTCCTGATGAGATACTAGAGAAGCGAACCAAATTCGT
*
85445 TTTCCTGATGAGATA-TAGAGAAGC
1 CTTCCTGATGAGATACTAGAGAAGC
85469 AAATTGAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 1 0.02
37 53 0.98
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (38 bp):
CTTCCTGATGAGATACTAGAGAAGCGAACCAAATTCGT
Found at i:85613 original size:242 final size:242
Alignment explanation
Indices: 85166--85826 Score: 961
Period size: 242 Copynumber: 2.7 Consensus size: 242
85156 AAACGGTGAG
*
85166 CTTCCTGATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
1 CTTCCTGATGAGATACAGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
*
85231 TGAAACAAATGACGTGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACTCATGC
66 TGAAACAAATGACGTGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGC
* ** * *
85296 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATGAGACACTGTGAAGCAGGTCGAAGTAAT
131 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATAAGACACTGAAAAGCAGGTAGAAGCAAT
* * *
85361 AAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGT
196 AAACGGTTAGCTTACTGATAAGATACTAAGAAGTGGACCAAATTCGT
* * *
85408 CTTCCTGATAAGATACAGAGAAGCGAACCAAATTCGTTTTCCTGATGAGATATAGAGAAGCAAAT
1 CTTCCTGATGAGATACAGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
* *
85473 TGAAACAAATGACGTGGTCATCTTCTTGGTGAGATACTAAGAAGAAGACCAAATCAAACCCATGC
66 TGAAACAAATGACGTGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGC
** *
85538 TCGATGTGAGCAAATCTTCGAATCTTAGCTTCTTGATAAGACACTGAAAAGCCGGTAGAAGCAAT
131 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATAAGACACTGAAAAGCAGGTAGAAGCAAT
*
85603 AAACGGTTAGCTTACTGATAAGATACTGAGAAGTGGACCAAATTCGT
196 AAACGGTTAGCTTACTGATAAGATACTAAGAAGTGGACCAAATTCGT
* **
85650 CTTCCTGATGAGATACAGAGAAGCGGACCAAATTC-TCCTTCCTGATGAGATACAGAGAAGCGGA
1 CTTCCTGATGAGATACAGAGAAGCGAACCAAATTCGT-CTTCCTGATGAGATACAGAGAAGCAAA
* * * * * * * *
85714 CTAAAACAAAGGACGTGATCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAGCCCACG
65 TTGAAACAAATGACGTGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATG
* * * * * *
85779 CTCGA--TGAACAAATCTTC-AAACCCAGTTTCCTGTTGAGACACTGAAAA
130 CTCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATAAGACACTGAAAA
85827 ACGGGTCGAA
Statistics
Matches: 375, Mismatches: 43, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
239 23 0.06
240 12 0.03
241 1 0.00
242 339 0.90
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (242 bp):
CTTCCTGATGAGATACAGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
TGAAACAAATGACGTGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGC
TCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATAAGACACTGAAAAGCAGGTAGAAGCAAT
AAACGGTTAGCTTACTGATAAGATACTAAGAAGTGGACCAAATTCGT
Found at i:85658 original size:37 final size:37
Alignment explanation
Indices: 85617--85714 Score: 153
Period size: 37 Copynumber: 2.6 Consensus size: 37
85607 GGTTAGCTTA
* * *
85617 CTGATAAGATACTGAGAAGTGGACCAAATTCGT-CTTC
1 CTGATGAGATACAGAGAAGCGGACCAAATTC-TCCTTC
85654 CTGATGAGATACAGAGAAGCGGACCAAATTCTCCTTC
1 CTGATGAGATACAGAGAAGCGGACCAAATTCTCCTTC
85691 CTGATGAGATACAGAGAAGCGGAC
1 CTGATGAGATACAGAGAAGCGGAC
85715 TAAAACAAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 1 0.02
37 56 0.98
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (37 bp):
CTGATGAGATACAGAGAAGCGGACCAAATTCTCCTTC
Found at i:86356 original size:17 final size:17
Alignment explanation
Indices: 86334--86384 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
86324 AACTTTTCTT
86334 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
* *
86351 TTAAGTTTAAAATTAAT
1 TTAAGTTTAAATTTAAA
86368 TTGAA-TTTAAAATTTAA
1 TT-AAGTTT-AAATTTAA
86385 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:87085 original size:3 final size:3
Alignment explanation
Indices: 87077--87117 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
87067 TTGATAGCAT
87077 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
87118 GTAAATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:88186 original size:29 final size:29
Alignment explanation
Indices: 88135--88388 Score: 227
Period size: 29 Copynumber: 8.8 Consensus size: 29
88125 AGAGGTCCCT
*** *
88135 AAACTTCCAAAAATTATGTTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* *
88165 -AACTTCCAAAAATCCCACTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTTACCTCG
* * *
88194 AAACTTCCAAAAATTACATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* * *
88223 AAACTTTCAAAAA-TCACA---TGACCCCG
1 AAACTTCCAAAAATTC-CATTTTTACCTCG
*
88249 AAATTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
88279 AAACTTCCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
88308 AAACTTCCAAAAATCCCGTTTTTGATCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
88338 AAACTTCCAAAAATTCCATTTTTGCCCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
88368 -AACTTCC-AAAATCTCCATTTT
1 AAACTTCCAAAAAT-TCCATTTT
88389 CGACGTCAAA
Statistics
Matches: 185, Mismatches: 27, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
26 19 0.10
27 2 0.01
28 6 0.03
29 80 0.43
30 78 0.42
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:88201 original size:30 final size:30
Alignment explanation
Indices: 88135--88388 Score: 246
Period size: 30 Copynumber: 8.7 Consensus size: 30
88125 AGAGGTCCCT
* *
88135 AAACTTCCAAAAATT--ATGTTTTTACCCCCG
1 AAACTTCCAAAAATTCCAT-TTTTGA-CCTCG
* *
88165 -AACTTCCAAAAATCCCACTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
88194 AAACTTCCAAAAATTACATTTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
* *
88223 AAACTTTCAAAAA-TCACA----TGACCCCG
1 AAACTTCCAAAAATTC-CATTTTTGACCTCG
*
88249 AAATTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
88279 AAACTTCCAAAAATTCCATTTTT-ACCCTC-
1 AAACTTCCAAAAATTCCATTTTTGA-CCTCG
* * *
88308 AAACTTCCAAAAATCCCGTTTTTGATCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
*
88338 AAACTTCCAAAAATTCCATTTTTGCCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
88368 -AACTTCC-AAAATCTCCATTTT
1 AAACTTCCAAAAAT-TCCATTTT
88389 CGACGTCAAA
Statistics
Matches: 187, Mismatches: 23, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
25 1 0.01
26 18 0.10
27 2 0.01
28 6 0.03
29 75 0.40
30 84 0.45
31 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:88228 original size:59 final size:60
Alignment explanation
Indices: 88135--88378 Score: 238
Period size: 59 Copynumber: 4.2 Consensus size: 60
88125 AGAGGTCCCT
** *
88135 AAACTTCCAAAAATTATGTTTTT-ACCCCCG-AACTTCCAAAAATCCCACTTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTTGA-CCCCGAAACTTCCAAAAATTCCACTTTTGACCTCG
* * * *
88194 AAACTTCCAAAAATTACATTTTT-ACCCCTAAACTTTCAAAAA-T-CAC--ATGACCCCG
1 AAACTTCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTCCACTTTTGACCTCG
* * * *
88249 AAATTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCA-TTTTTACCCTC-
1 AAACTTCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTCCACTTTTGA-CCTCG
** * * * * *
88308 AAACTTCCAAAAATCCCGTTTTTGATCTCGAAACTTCCAAAAATTCCATTTTTGCCCTCG
1 AAACTTCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTCCACTTTTGACCTCG
88368 -AACTTCCAAAA
1 AAACTTCCAAAA
88379 TCTCCATTTT
Statistics
Matches: 155, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
55 28 0.18
56 16 0.10
57 4 0.03
58 6 0.04
59 94 0.61
60 7 0.05
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (60 bp):
AAACTTCCAAAAATTACATTTTTGACCCCGAAACTTCCAAAAATTCCACTTTTGACCTCG
Found at i:97119 original size:72 final size:72
Alignment explanation
Indices: 97038--97178 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
97028 TACACCAAAA
97038 TATCACTTACAAGTTAATATTTTATCCAAAGATAAAATATTAATGGAGTGTCCGATATTTTGATA
1 TATCACTTACAAGTTAATATTTTATCCAAAGATAAAATATTAATGGAGTGTCCGATATTTTGATA
97103 TGAGGTT
66 TGAGGTT
*
97110 TATCACTTACAAGTTAATATTTTATCCAAAGATAAAATATTAATGGAGTGTCCGATATTTTGGTA
1 TATCACTTACAAGTTAATATTTTATCCAAAGATAAAATATTAATGGAGTGTCCGATATTTTGATA
97175 TGAG
66 TGAG
97179 ATTTTCCTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (72 bp):
TATCACTTACAAGTTAATATTTTATCCAAAGATAAAATATTAATGGAGTGTCCGATATTTTGATA
TGAGGTT
Found at i:102237 original size:25 final size:24
Alignment explanation
Indices: 102203--102256 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
102193 GTTTTGTATT
*
102203 AATATTTATATTAACATTAAATAA
1 AATAATTATATTAACATTAAATAA
*
102227 ATATAATTATATTAATATTAAATAA
1 A-ATAATTATATTAACATTAAATAA
102252 AATAA
1 AATAA
102257 AAATGTCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAATTATATTAACATTAAATAA
Found at i:108440 original size:2 final size:2
Alignment explanation
Indices: 108435--108464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
108425 AAATAAATAA
108435 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
108465 GTTAGATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112825 original size:38 final size:38
Alignment explanation
Indices: 112774--112849 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
112764 CAATTTAATT
112774 TTGACTCTTTAAATTTTCTTTTTTTCTTGATTTCGCCC
1 TTGACTCTTTAAATTTTCTTTTTTTCTTGATTTCGCCC
112812 TTGACTCTTTAAATTTTCTTTTTTTCTTGATTTCGCCC
1 TTGACTCTTTAAATTTTCTTTTTTTCTTGATTTCGCCC
112850 CTGCTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.13, C:0.21, G:0.08, T:0.58
Consensus pattern (38 bp):
TTGACTCTTTAAATTTTCTTTTTTTCTTGATTTCGCCC
Found at i:113267 original size:27 final size:28
Alignment explanation
Indices: 113226--113283 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 28
113216 TGCATATGAA
113226 TTTTTTTTTCACATCA-AATTCAGTGTT
1 TTTTTTTTTCACATCACAATTCAGTGTT
113253 TTTTTTTTTGC-CATCATCGAATTCAGTGTT
1 TTTTTTTTT-CACATCA-C-AATTCAGTGTT
113283 T
1 T
113284 AATTTAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 14 0.52
28 1 0.04
30 12 0.44
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (28 bp):
TTTTTTTTTCACATCACAATTCAGTGTT
Found at i:113276 original size:30 final size:27
Alignment explanation
Indices: 113226--113283 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 27
113216 TGCATATGAA
113226 TTTTTTTTTCACATCAAATTCAGTGTT
1 TTTTTTTTTCACATCAAATTCAGTGTT
*
113253 TTTTTTTTTGCCATCATCGAATTCAGTGTT
1 TTTTTTTTT--CA-CATCAAATTCAGTGTT
113283 T
1 T
113284 AATTTAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.33
29 2 0.07
30 16 0.59
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (27 bp):
TTTTTTTTTCACATCAAATTCAGTGTT
Found at i:113806 original size:16 final size:16
Alignment explanation
Indices: 113755--113807 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
113745 AAGTAACCCG
113755 ATAACATAATAACATGTAA
1 ATAA-ATAAT-ACAT-TAA
* * *
113774 AAAAATAATAAAATAA
1 ATAAATAATACATTAA
113790 ATAAATAATACATTAA
1 ATAAATAATACATTAA
113806 AT
1 AT
113808 TAAAAATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 18 0.64
17 2 0.07
18 5 0.18
19 3 0.11
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (16 bp):
ATAAATAATACATTAA
Found at i:125435 original size:65 final size:65
Alignment explanation
Indices: 125330--125461 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 65
125320 TCCACGTTGG
125330 AACAGGAAAAAATGGATGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAAC
1 AACAGGAAAAAATGGATGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAAC
**
125395 AACAGGAAAAAAT-GATTGACACCCATTCTTGATTGTAATGTTCTTTTAAGGATAATTCGACAAA
1 AACAGGAAAAAATGGA-TGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAA
125459 C
65 C
125460 AA
1 AA
125462 GGAGGAAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 2 0.03
65 62 0.97
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (65 bp):
AACAGGAAAAAATGGATGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAAC
Found at i:128819 original size:31 final size:31
Alignment explanation
Indices: 128760--128819 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
128750 GCTATTGAAT
* * *
128760 TATTCAAAATTTTTTATTTAAATCACTAAAC
1 TATTCAAAAGTTTTAATTTAAATAACTAAAC
* *
128791 TATTCAATAGTTTTAATTTAAGTAACTAA
1 TATTCAAAAGTTTTAATTTAAATAACTAA
128820 GTTATTAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (31 bp):
TATTCAAAAGTTTTAATTTAAATAACTAAAC
Found at i:133770 original size:20 final size:20
Alignment explanation
Indices: 133745--133784 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
133735 TTAGAAAGGG
133745 ACACTAAGTTTGTCTCCACA
1 ACACTAAGTTTGTCTCCACA
133765 ACACTAAGTTTGTCTCCACA
1 ACACTAAGTTTGTCTCCACA
133785 CGGTGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (20 bp):
ACACTAAGTTTGTCTCCACA
Found at i:135939 original size:110 final size:109
Alignment explanation
Indices: 135818--136021 Score: 266
Period size: 109 Copynumber: 1.9 Consensus size: 109
135808 CGAACCGAAA
* * *
135818 TTTTTCAGTTAATTCTGTCAATTAA-TCGAATTAATAAAAATTTATATGTGTTTTTATTTATTTT
1 TTTTTCAGTTAATTCGGTCAATTAAGT-AAATTAATAAAAATTTATACGT-TTTTTATTTATTTT
135882 TGATTAAAACAAATATAAAACATATAAAAAAATAATTGAATTAAAT
64 TGATTAAAACAAATATAAAACATATAAAAAAATAATTGAATTAAAT
* ** ** * *
135928 TTTTTCGGTTAATTCGGTCGGTTAAGTAAATTAATCGAAATTTATACGTTTTTTTTTTTTTTTTG
1 TTTTTCAGTTAATTCGGTCAATTAAGTAAATTAATAAAAATTTATACGTTTTTTATTTATTTTTG
* * *
135993 GTTAAAACAAGTATAAAATATATAAAAAA
66 ATTAAAACAAATATAAAACATATAAAAAA
136022 TTAACCGACT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
109 40 0.50
110 39 0.49
111 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (109 bp):
TTTTTCAGTTAATTCGGTCAATTAAGTAAATTAATAAAAATTTATACGTTTTTTATTTATTTTTG
ATTAAAACAAATATAAAACATATAAAAAAATAATTGAATTAAAT
Found at i:149083 original size:21 final size:22
Alignment explanation
Indices: 149059--149106 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
149049 ATTTTGATAA
*
149059 ATTTTGAG-ATTTAATTATTAT
1 ATTTTAAGAATTTAATTATTAT
149080 ATTTTAAGAATTTAATTATTAT
1 ATTTTAAGAATTTAATTATTAT
149102 -TTTTA
1 ATTTTA
149107 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
ATTTTAAGAATTTAATTATTAT
Found at i:149758 original size:17 final size:17
Alignment explanation
Indices: 149714--149755 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
149704 GTTTATTTTC
* *
149714 TTATATAGT-TTTAAAT
1 TTATATATTATTTAAAA
149730 TTATATATTATTTAAAA
1 TTATATATTATTTAAAA
149747 TTATCATAT
1 TTAT-ATAT
149756 ATTGAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 10 0.45
18 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTATATATTATTTAAAA
Found at i:150409 original size:19 final size:20
Alignment explanation
Indices: 150368--150409 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
150358 AGAAAATTAA
*
150368 AATATAAAAAAATAAGTATTG
1 AATATAAAAAAATAAG-AGTG
*
150389 AATATAAAAAATTAAG-GTG
1 AATATAAAAAAATAAGAGTG
150408 AA
1 AA
150410 AAAATACCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (20 bp):
AATATAAAAAAATAAGAGTG
Found at i:156060 original size:18 final size:17
Alignment explanation
Indices: 156037--156094 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
156027 CTCAAATGTG
156037 TTTTTGAAAAAAAAAATA
1 TTTTTG-AAAAAAAAATA
*
156055 TTTTTGAAATAAAAATA
1 TTTTTGAAAAAAAAATA
* *
156072 TTATT--AAACAAAATA
1 TTTTTGAAAAAAAAATA
*
156087 CTTTTGAA
1 TTTTTGAA
156095 TTTTTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 11 0.34
17 15 0.47
18 6 0.19
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (17 bp):
TTTTTGAAAAAAAAATA
Found at i:156181 original size:19 final size:18
Alignment explanation
Indices: 156153--156201 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
156143 AGTCAAAAAG
* *
156153 AAATAATTTTTTTTCTCAA
1 AAATACTTTTTTAT-TCAA
*
156172 AAATACTTTTTAATTCAA
1 AAATACTTTTTTATTCAA
156190 AAAT-CTTTTTTA
1 AAATACTTTTTTA
156202 AAGAATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 7 0.27
18 8 0.31
19 11 0.42
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATACTTTTTTATTCAA
Found at i:160193 original size:236 final size:237
Alignment explanation
Indices: 159895--160347 Score: 829
Period size: 236 Copynumber: 1.9 Consensus size: 237
159885 CTAAAATGAA
159895 AATATTCTTTGTTTAATCCCTTCAAAAATGATGAAATTATAAATTAATATGAAATAAATCTATAT
1 AATATTCTTTGTTTAATCCCTTCAAAAATGATGAAATTATAAATTAATATGAAATAAATCTATAT
159960 TTAATCTATGAAAAAGTATAATTAAATTTCAACCCTGCTAAAAG-TTTTTTTGGATTTGCCCCTA
66 TTAATCTATGAAAAAGTATAATTAAATTTCAACCCTGCTAAAAGTTTTTTTTGGATTTGCCCCTA
*
160024 C-CTGTACGGATGCCGTGAACAGGTTTCTTTGGTTCTTTTTTATCATTCATTTGTTGTGTTTTAT
131 CAC-GTACGGATGCCGTGAACAGGTTTCTTTGATTCTTTTTTATCATTCATTTGTTGTGTTTTAT
160088 ATTGATTTGATTTTATATTATAACTAATCATACATCAATTTGT
195 ATTGATTTGATTTTATATTATAACTAATCATACATCAATTTGT
*
160131 AATATTTTTTGTTTAATCCCTTCAAAAATGATGAAATTATAAATTAATATGAAATAAATCTATAT
1 AATATTCTTTGTTTAATCCCTTCAAAAATGATGAAATTATAAATTAATATGAAATAAATCTATAT
160196 TTAATCTATGAAAAAGTATAATTAAATTTCAACCCTGCTAAAAGTTTTTTTTGGATTTGCCCCTA
66 TTAATCTATGAAAAAGTATAATTAAATTTCAACCCTGCTAAAAGTTTTTTTTGGATTTGCCCCTA
* *
160261 CACGTACGGATGCCGTGAACAGGTTTTTTTTATTCTTTTTTATCATTCATTTGTTGTGTTTTATA
131 CACGTACGGATGCCGTGAACAGGTTTCTTTGATTCTTTTTTATCATTCATTTGTTGTGTTTTATA
* *
160326 TTTATTTGGTTTTATATTATAA
196 TTGATTTGATTTTATATTATAA
160348 TTGACCATTG
Statistics
Matches: 209, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
236 108 0.52
237 100 0.48
238 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (237 bp):
AATATTCTTTGTTTAATCCCTTCAAAAATGATGAAATTATAAATTAATATGAAATAAATCTATAT
TTAATCTATGAAAAAGTATAATTAAATTTCAACCCTGCTAAAAGTTTTTTTTGGATTTGCCCCTA
CACGTACGGATGCCGTGAACAGGTTTCTTTGATTCTTTTTTATCATTCATTTGTTGTGTTTTATA
TTGATTTGATTTTATATTATAACTAATCATACATCAATTTGT
Found at i:167105 original size:24 final size:26
Alignment explanation
Indices: 167078--167134 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
167068 AATATTTGAT
167078 ATTTGAACTTAAC-ACTTTTT-TCTA
1 ATTTGAACTTAACTACTTTTTATCTA
* *
167102 ATTTGTACTTAACTATTTTTTGATCTA
1 ATTTGAACTTAACTACTTTTT-ATCTA
167129 ATTTGA
1 ATTTGA
167135 TACTCAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.44
25 6 0.22
27 9 0.33
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (26 bp):
ATTTGAACTTAACTACTTTTTATCTA
Found at i:167160 original size:30 final size:30
Alignment explanation
Indices: 167125--167187 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
167115 TATTTTTTGA
167125 TCTAATTTGATA-CTCAAACTCGACACGTTT
1 TCTAATTTGATACCT-AAACTCGACACGTTT
* * *
167155 TCTAATTTGCTACCTAAACTTGACACTTTT
1 TCTAATTTGATACCTAAACTCGACACGTTT
167185 TCT
1 TCT
167188 TAAAGTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (30 bp):
TCTAATTTGATACCTAAACTCGACACGTTT
Found at i:168408 original size:29 final size:30
Alignment explanation
Indices: 168350--168409 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
168340 GATGAGAGAG
*
168350 GAGTAAAAAATTTTGGGGGAAAGTGCAAAA
1 GAGTAAAAAATTTTGGGGGAAAGTGAAAAA
* *
168380 GAGT-AAAAGTTTTGGGGGAAAAGTAAAAAA
1 GAGTAAAAAATTTTGGGGG-AAAGTGAAAAA
168410 AATTTGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.30, T:0.20
Consensus pattern (30 bp):
GAGTAAAAAATTTTGGGGGAAAGTGAAAAA
Found at i:170627 original size:20 final size:20
Alignment explanation
Indices: 170602--170668 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
170592 GATGATGATT
170602 ATAATTTTAAAATAATTTT--A
1 ATAATTTT--AATAATTTTAAA
170622 ATAATTTT-AT-ATTTTAAAAA
1 ATAATTTTAATAATTTT--AAA
170642 ATAATTTTAATAATTTTAAA
1 ATAATTTTAATAATTTTAAA
*
170662 ATTATTT
1 ATAATTT
170669 GCTGACATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.12
17 2 0.05
20 26 0.65
21 2 0.05
22 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTTTAATAATTTTAAA
Found at i:186934 original size:137 final size:137
Alignment explanation
Indices: 186688--186961 Score: 512
Period size: 137 Copynumber: 2.0 Consensus size: 137
186678 CCATTCAAAC
186688 AAGCCAAGGGCTATCTGAAGCTTATAAAAGCCTTCTTTTTAAGACCCCATTAATAATGTTGGTAT
1 AAGCCAAGGGCTATCTGAAGCTTATAAAAGCCTTCTTTTTAAGACCCCATTAATAATGTTGGTAT
*
186753 GAGTAGAGGATATTTTCCATTGGCACATGGTAGTGAGTGGTGGGGAATGCTCTCAGCATTCCTGC
66 GAATAGAGGATATTTTCCATTGGCACATGGTAGTGAGTGGTGGGGAATGCTCTCAGCATTCCTGC
186818 CAAACAT
131 CAAACAT
186825 AAGCCAAGGGCTATCTGAAGCTTATAAAAGCCTTCTTTTTAAGACCCCATTAATAATGTTGGTAT
1 AAGCCAAGGGCTATCTGAAGCTTATAAAAGCCTTCTTTTTAAGACCCCATTAATAATGTTGGTAT
* * *
186890 GAATAGAGGATATTTTCCGTTGGCACATGGTAGTGAGTGGTGGGGAGTGCTCTCAGCATTCTTGC
66 GAATAGAGGATATTTTCCATTGGCACATGGTAGTGAGTGGTGGGGAATGCTCTCAGCATTCCTGC
186955 CAAACAT
131 CAAACAT
186962 TTGATGACTA
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (137 bp):
AAGCCAAGGGCTATCTGAAGCTTATAAAAGCCTTCTTTTTAAGACCCCATTAATAATGTTGGTAT
GAATAGAGGATATTTTCCATTGGCACATGGTAGTGAGTGGTGGGGAATGCTCTCAGCATTCCTGC
CAAACAT
Found at i:188637 original size:3 final size:3
Alignment explanation
Indices: 188629--188670 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
188619 CCGCTATAAG
* *
188629 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTT TTC TTT TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
188671 ATTTTTCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:192723 original size:6 final size:6
Alignment explanation
Indices: 192708--192737 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
192698 ATCCTCTGTT
*
192708 TTTTTG TTTTTT TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
192738 GATAATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTTG
Found at i:193001 original size:30 final size:30
Alignment explanation
Indices: 192965--193026 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
192955 TACATTTCAG
*
192965 TCCCTCAACTTTAAAAATATGACAAAACAA
1 TCCCTCAACTTCAAAAATATGACAAAACAA
* *
192995 TCCCTCAACTTCGAAAATGTGACAAAACAA
1 TCCCTCAACTTCAAAAATATGACAAAACAA
193025 TC
1 TC
193027 TTTTTCCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (30 bp):
TCCCTCAACTTCAAAAATATGACAAAACAA
Found at i:195841 original size:25 final size:24
Alignment explanation
Indices: 195792--195940 Score: 107
Period size: 23 Copynumber: 6.4 Consensus size: 24
195782 ACACTAGCGC
* *
195792 GCTCTCTGT-TTAGCACATCT-CGT
1 GCTCTCTGTATTAGCAC-TTTGTGT
*
195815 GCTCTTTGTTATTAGCACTTTGTGT
1 GCTCTCTG-TATTAGCACTTTGTGT
*
195840 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTTTGTGT
* *
195863 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTTTGTGT
** *
195886 GCTCTCTGTTACCCAGCAC-TTATGT
1 GCTCTCTG-TA-TTAGCACTTTGTGT
*
195911 GCTCTCTG--TTAGTACTTTG-GT
1 GCTCTCTGTATTAGCACTTTGTGT
*
195932 ACTCTCTGT
1 GCTCTCTGT
195941 TTGTTCCGTA
Statistics
Matches: 99, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
21 13 0.13
22 2 0.02
23 47 0.47
24 4 0.04
25 28 0.28
26 5 0.05
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTTTGTGT
Found at i:195857 original size:23 final size:22
Alignment explanation
Indices: 195826--195941 Score: 110
Period size: 23 Copynumber: 5.1 Consensus size: 22
195816 CTCTTTGTTA
195826 TTAGCACTTTGTGTGCTCTCTG
1 TTAGCACTTTGTGTGCTCTCTG
* *
195848 ATTAGTACTTTGTGTACTCTCTG
1 -TTAGCACTTTGTGTGCTCTCTG
*
195871 TTTAGCACTGTGTGTGCTCTCTG
1 -TTAGCACTTTGTGTGCTCTCTG
*
195894 TTACCCAGCAC-TTATGTGCTCTCTG
1 TT----AGCACTTTGTGTGCTCTCTG
* *
195919 TTAGTACTTTG-GTACTCTCTG
1 TTAGCACTTTGTGTGCTCTCTG
195940 TT
1 TT
195942 TGTTCCGTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
21 15 0.19
22 4 0.05
23 39 0.51
25 14 0.18
26 5 0.06
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (22 bp):
TTAGCACTTTGTGTGCTCTCTG
Found at i:195912 original size:71 final size:69
Alignment explanation
Indices: 195793--195942 Score: 196
Period size: 71 Copynumber: 2.1 Consensus size: 69
195783 CACTAGCGCG
* ** *
195793 CTCTCTGTTTAGCACATCTCGTGCTCTTTGTTATTAGCACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTGTTTAGCACATCTCGTGCTCTCTGTTACCAGCACTTTATGTGCTCTCTG-TTAGTACTT
195858 TGTGTA
65 TG-GTA
* *
195864 CTCTCTGTTTAGCAC-TGTGTGTGCTCTCTGTTACCCAGCAC-TTATGTGCTCTCTGTTAGTACT
1 CTCTCTGTTTAGCACATCT-CGTGCTCTCTGTTA-CCAGCACTTTATGTGCTCTCTGTTAGTACT
195927 TTGGTA
64 TTGGTA
195933 CTCTCTGTTT
1 CTCTCTGTTT
195943 GTTCCGTATA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
69 13 0.18
70 13 0.18
71 40 0.56
72 5 0.07
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACATCTCGTGCTCTCTGTTACCAGCACTTTATGTGCTCTCTGTTAGTACTTT
GGTA
Found at i:196428 original size:22 final size:22
Alignment explanation
Indices: 196383--196456 Score: 103
Period size: 23 Copynumber: 3.3 Consensus size: 22
196373 GAAACAATAA
196383 GCACACACAGTGCAATCCAGTAG
1 GCACACACAGTGCAAT-CAGTAG
196406 GCACACACAGTGCAATCAGTAG
1 GCACACACAGTGCAATCAGTAG
* * *
196428 GCGCACATAGCGCAAATCAGTAG
1 GCACACACAGTGC-AATCAGTAG
196451 GCACAC
1 GCACAC
196457 GAGGTGCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.35
23 30 0.65
ACGTcount: A:0.35, C:0.30, G:0.23, T:0.12
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:198451 original size:30 final size:31
Alignment explanation
Indices: 198387--198458 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
198377 ACAACAAGAG
* *
198387 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACTTTTCGATAACTTGAGT
*
198418 GACTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCGATAACTTGAGT
198448 GACTGTTTTGT
1 GACTGTTTTGT
198459 TAAATGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.49
31 14 0.38
32 5 0.14
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAACTTGAGT
Found at i:199121 original size:43 final size:44
Alignment explanation
Indices: 199073--199158 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
199063 TTAAGTTAAA
199073 AATTCAATATACC-AAATAGATATTAACAATAACATATAATTCT
1 AATTCAATATACCAAAATAGATATTAACAATAACATATAATTCT
199116 AATTCAATATACCAAAATAGATATTAACAATAACATATAATTC
1 AATTCAATATACCAAAATAGATATTAACAATAACATATAATTC
199159 AAGAATACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 13 0.31
44 29 0.69
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.31
Consensus pattern (44 bp):
AATTCAATATACCAAAATAGATATTAACAATAACATATAATTCT
Found at i:200001 original size:10 final size:10
Alignment explanation
Indices: 199986--200012 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
199976 TTAAATATAT
199986 AAAAAAAATA
1 AAAAAAAATA
199996 AAAAAAAATA
1 AAAAAAAATA
200006 AAAAAAA
1 AAAAAAA
200013 CACGTGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:211766 original size:17 final size:19
Alignment explanation
Indices: 211736--211772 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
211726 GTTGAGGGAG
211736 AGAGAAGAAGAAC-AGAAA
1 AGAGAAGAAGAACAAGAAA
*
211754 AGAG-AGAATAACAAGAAA
1 AGAGAAGAAGAACAAGAAA
211772 A
1 A
211773 ACAGTTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.03
Consensus pattern (19 bp):
AGAGAAGAAGAACAAGAAA
Found at i:217452 original size:5 final size:5
Alignment explanation
Indices: 217438--217475 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
217428 ACAATCTCTC
* *
217438 TTTCT TTTCT CTTCT TTTCT TTTCT CTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
217476 TATTCCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:217485 original size:15 final size:15
Alignment explanation
Indices: 217438--217475 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
217428 ACAATCTCTC
217438 TTTCTTTTCTCTTCT
1 TTTCTTTTCTCTTCT
217453 TTTCTTTTCTCTTCT
1 TTTCTTTTCTCTTCT
217468 TTTCTTTT
1 TTTCTTTT
217476 TATTCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCTCTTCT
Found at i:247678 original size:22 final size:22
Alignment explanation
Indices: 247630--247718 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 22
247620 TTCATTTAAT
* *
247630 TTAATCGAACATGTTTACAAACA
1 TTAATCGAACATGTTCAC-GACA
247653 TTAATCGAACATGTTCACGACA
1 TTAATCGAACATGTTCACGACA
* *
247675 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACG-ACA
* *
247698 TATAATTGAACACGTTCACGA
1 T-TAATCGAACATGTTCACGA
247719 ACAATGTTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
22 20 0.36
23 22 0.39
24 14 0.25
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (22 bp):
TTAATCGAACATGTTCACGACA
Found at i:247709 original size:46 final size:45
Alignment explanation
Indices: 247630--247718 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
247620 TTCATTTAAT
* * *
247630 TTAATCGAACATGTTTACAAACATTAATCGAACATGTTCACGACA
1 TTAAACGAACATGTTCACAAACATTAATCGAACACGTTCACGACA
** *
247675 TTAAACGAACATGTTCATGAACATATAATTGAACACGTTCACGA
1 TTAAACGAACATGTTCACAAACAT-TAATCGAACACGTTCACGA
247719 ACAATGTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 20 0.54
46 17 0.46
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (45 bp):
TTAAACGAACATGTTCACAAACATTAATCGAACACGTTCACGACA
Found at i:255395 original size:22 final size:22
Alignment explanation
Indices: 255369--255410 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
255359 AACAAAAAAT
*
255369 AAATAAACATATTTTAAATATA
1 AAATAAACATATTATAAATATA
**
255391 AAATAATTATATTATAAATA
1 AAATAAACATATTATAAATA
255411 ATAACATCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATAAACATATTATAAATATA
Found at i:266613 original size:17 final size:18
Alignment explanation
Indices: 266581--266614 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
266571 AATTTAATAA
*
266581 TTAATTTTATTATCACTG
1 TTAATTTAATTATCACTG
266599 TTAATTTAATT-TCACT
1 TTAATTTAATTATCACT
266615 TAAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (18 bp):
TTAATTTAATTATCACTG
Found at i:279244 original size:85 final size:85
Alignment explanation
Indices: 279101--279266 Score: 332
Period size: 85 Copynumber: 2.0 Consensus size: 85
279091 CACTGCACAT
279101 TCACTAGTCACCTTTTTAGCTCCAATGCTACAAGTAAATCATAAGTTAGCACAATAATTACATTG
1 TCACTAGTCACCTTTTTAGCTCCAATGCTACAAGTAAATCATAAGTTAGCACAATAATTACATTG
279166 CTACTAATAAAACTAGTAAA
66 CTACTAATAAAACTAGTAAA
279186 TCACTAGTCACCTTTTTAGCTCCAATGCTACAAGTAAATCATAAGTTAGCACAATAATTACATTG
1 TCACTAGTCACCTTTTTAGCTCCAATGCTACAAGTAAATCATAAGTTAGCACAATAATTACATTG
279251 CTACTAATAAAACTAG
66 CTACTAATAAAACTAG
279267 CAACATCAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (85 bp):
TCACTAGTCACCTTTTTAGCTCCAATGCTACAAGTAAATCATAAGTTAGCACAATAATTACATTG
CTACTAATAAAACTAGTAAA
Found at i:294135 original size:21 final size:23
Alignment explanation
Indices: 294015--294133 Score: 136
Period size: 23 Copynumber: 5.3 Consensus size: 23
294005 ACTAGTGCGT
* *
294015 TCTCTGTTTAGCACGTTT-CGTGC
1 TCTCTGATTAGCAC-TTTGTGTGC
* * *
294038 CCTCTGATTAGTACTTTATGTGC
1 TCTCTGATTAGCACTTTGTGTGC
294061 TCTCTGATTAGCACTTTGTGTGC
1 TCTCTGATTAGCACTTTGTGTGC
294084 TCTCTGATTAGCACTTTGTGTGC
1 TCTCTGATTAGCACTTTGTGTGC
* * *
294107 TCTTTG-TTAGTACTTTG-GTTC
1 TCTCTGATTAGCACTTTGTGTGC
294128 TCTCTG
1 TCTCTG
294134 TTTGTTCCGT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.10
22 13 0.15
23 63 0.75
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (23 bp):
TCTCTGATTAGCACTTTGTGTGC
Found at i:312008 original size:21 final size:20
Alignment explanation
Indices: 311983--312026 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
311973 TTTTTTTCTA
311983 TTTTCTTTTCTTTCTTCATTT
1 TTTTCTTTTCTTTC-TCATTT
* *
312004 TTTTCTTTTTTTTCTCCTTT
1 TTTTCTTTTCTTTCTCATTT
312024 TTT
1 TTT
312027 CCACCTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTCTTTCTCATTT
Found at i:315469 original size:24 final size:23
Alignment explanation
Indices: 315442--315494 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
315432 TTATATAATG
* * *
315442 AAAATATTTATTAAAAATTTATAT
1 AAAATATTT-TCAAAAAATTACAT
315466 AAAATTATTTTCAAAAAATTACAT
1 AAAA-TATTTTCAAAAAATTACAT
315490 AAAAT
1 AAAAT
315495 TAATTGATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 19 0.76
25 5 0.20
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATATTTTCAAAAAATTACAT
Found at i:315863 original size:24 final size:24
Alignment explanation
Indices: 315817--315864 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
315807 TTAAATTCGG
*
315817 TTTTATTTAAATTTAATTTTAAAT
1 TTTTATTTAAATTTAATTATAAAT
*
315841 TTTTATTTTAA-TTAATTAATAAAT
1 TTTTATTTAAATTTAATT-ATAAAT
315865 ATTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATTTAAATTTAATTATAAAT
Found at i:316667 original size:13 final size:13
Alignment explanation
Indices: 316651--316675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
316641 TAACTTTTGT
316651 TTTTTTTAATATG
1 TTTTTTTAATATG
316664 TTTTTTTAATAT
1 TTTTTTTAATAT
316676 ATTTAAATAA
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTTTTAATATG
Found at i:321525 original size:31 final size:32
Alignment explanation
Indices: 321490--321560 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
321480 ATGAGTCAAG
* * *
321490 ATTAAAATTTTAA-AATT-AAAAATATATAATA
1 ATTAAAATTTGAACAATTCAAAAAT-TAAAAAA
321521 ATTAAAA-TTGAACAATTCAAAAATTAAAAAA
1 ATTAAAATTTGAACAATTCAAAAATTAAAAAA
321552 ATTAAAATT
1 ATTAAAATT
321561 ATCAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.12
31 23 0.68
32 7 0.21
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (32 bp):
ATTAAAATTTGAACAATTCAAAAATTAAAAAA
Found at i:321553 original size:9 final size:9
Alignment explanation
Indices: 321539--321586 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
321529 TGAACAATTC
321539 AAAAATTAA
1 AAAAATTAA
321548 AAAAATTAA
1 AAAAATTAA
** *
321557 AATTATCAA
1 AAAAATTAA
*
321566 AATAAATTAT
1 AA-AAATTAA
321576 AAAAATTAA
1 AAAAATTAA
321585 AA
1 AA
321587 CCACAAATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 25 0.83
10 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTAA
Found at i:321558 original size:15 final size:15
Alignment explanation
Indices: 321490--321586 Score: 76
Period size: 15 Copynumber: 6.5 Consensus size: 15
321480 ATGAGTCAAG
*
321490 ATTAAAATT-TTAAA
1 ATTAAAATTATAAAA
*
321504 ATTAAAAATATATAATA
1 ATT-AAAAT-TATAAAA
* *
321521 ATTAAAATT-GAACA
1 ATTAAAATTATAAAA
*
321535 ATTCAAAAATTAAAAAA
1 ATT--AAAATTATAAAA
*
321552 ATTAAAATTATCAAA
1 ATTAAAATTATAAAA
321567 A-T-AAATTATAAAA
1 ATTAAAATTATAAAA
321580 ATTAAAA
1 ATTAAAA
321587 CCACAAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
13 11 0.17
14 11 0.17
15 20 0.30
16 12 0.18
17 12 0.18
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (15 bp):
ATTAAAATTATAAAA
Found at i:324272 original size:25 final size:23
Alignment explanation
Indices: 324256--324416 Score: 141
Period size: 23 Copynumber: 7.0 Consensus size: 23
324246 GTTATCTGTT
* * *
324256 ATTAGTACTGTGTGTGTTCTCTT
1 ATTAGTACTTTGTGTGCTCTCTG
* *
324279 ACTAGCACTTTGTGTGCTCTCTG
1 ATTAGTACTTTGTGTGCTCTCTG
324302 ATTAGTACTTTGTGTGCTCTCTG
1 ATTAGTACTTTGTGTGCTCTCTG
* *
324325 ATTAGTACTCTGTGTACTCTCTG
1 ATTAGTACTTTGTGTGCTCTCTG
* * *
324348 TTTAGCACTATGTGTGCTCTCTG
1 ATTAGTACTTTGTGTGCTCTCTG
* *
324371 -TTACCCAGCAC-TTATGTGCTCTCTG
1 ATT----AGTACTTTGTGTGCTCTCTG
*
324396 -TTAGTACTTTG-GTACTCTCTG
1 ATTAGTACTTTGTGTGCTCTCTG
324417 TTTGTTCTGT
Statistics
Matches: 115, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
21 13 0.11
22 4 0.03
23 79 0.69
25 14 0.12
26 5 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (23 bp):
ATTAGTACTTTGTGTGCTCTCTG
Found at i:333005 original size:2 final size:2
Alignment explanation
Indices: 332998--333027 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
332988 GGGCTAAGTT
332998 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
333028 GGAGGAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:339338 original size:8 final size:7
Alignment explanation
Indices: 339303--339340 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
339293 GCAAAAACCC
339303 TTTTTCT
1 TTTTTCT
339310 TTTTTCT
1 TTTTTCT
339317 TTTTT-T
1 TTTTTCT
*
339323 TCTTTCT
1 TTTTTCT
339330 TTTTATCT
1 TTTT-TCT
339338 TTT
1 TTT
339341 AGCCAATCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 5 0.19
7 16 0.59
8 6 0.22
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:347110 original size:2 final size:2
Alignment explanation
Indices: 347098--347140 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
347088 GGGAAAATAA
347098 AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
347139 AG
1 AG
347141 GGAGTGAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:380168 original size:28 final size:27
Alignment explanation
Indices: 380132--380184 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
380122 ATATATTTAT
380132 TAAACTATAAAATAATGAATTTTAAAAAA
1 TAAACTATAAAATAA-GAA-TTTAAAAAA
380161 TAAA-TATAAAATAAGAATTTAAAA
1 TAAACTATAAAATAAGAATTTAAAA
380185 CATTTGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.29
27 3 0.12
28 10 0.42
29 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (27 bp):
TAAACTATAAAATAAGAATTTAAAAAA
Found at i:380183 original size:13 final size:14
Alignment explanation
Indices: 380139--380184 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
380129 TATTAAACTA
380139 TAAAATAATGAATTT
1 TAAAATAATGAA-TT
* *
380154 TAAAA-AATAAATA
1 TAAAATAATGAATT
380167 TAAAATAA-GAATT
1 TAAAATAATGAATT
380180 TAAAA
1 TAAAA
380185 CATTTGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 14 0.54
14 7 0.27
15 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
TAAAATAATGAATT
Found at i:393715 original size:16 final size:17
Alignment explanation
Indices: 393694--393730 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
393684 TATTATGTTT
393694 TAATTTATTAATA-ATA
1 TAATTTATTAATATATA
*
393710 TAATTTGTTAATATATA
1 TAATTTATTAATATATA
393727 TAAT
1 TAAT
393731 CATCATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TAATTTATTAATATATA
Found at i:395575 original size:25 final size:25
Alignment explanation
Indices: 395547--395596 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
395537 AACGAAAAAT
395547 GAAAGAAAAAAAAAAAGAAAAAAGA
1 GAAAGAAAAAAAAAAAGAAAAAAGA
* * *
395572 GAAAGAAAGAAAGAAAGAAAGAAGA
1 GAAAGAAAAAAAAAAAGAAAAAAGA
395597 AGGAAGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (25 bp):
GAAAGAAAAAAAAAAAGAAAAAAGA
Found at i:395578 original size:4 final size:4
Alignment explanation
Indices: 395547--395594 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
395537 AACGAAAAAT
* * *
395547 GAAA GAAA AAAA AAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
395595 GAAGGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 36 0.92
5 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:395594 original size:12 final size:12
Alignment explanation
Indices: 395541--395591 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
395531 GGGACCAACG
*
395541 AAAAATGAAAGA
1 AAAAAAGAAAGA
*
395553 AAAAAAAAAAGA
1 AAAAAAGAAAGA
395565 AAAAAGAGAAAGA
1 AAAAA-AGAAAGA
*
395578 AAGAAAGAAAGA
1 AAAAAAGAAAGA
395590 AA
1 AA
395592 GAAGAAGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 24 0.71
13 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:395613 original size:9 final size:9
Alignment explanation
Indices: 395591--395627 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
395581 AAAGAAAGAA
395591 AGAAGAA-G
1 AGAAGAAGG
395599 -GAAGAAGG
1 AGAAGAAGG
395607 AGAAGAAGG
1 AGAAGAAGG
*
395616 GGAAGAAGG
1 AGAAGAAGG
395625 AGA
1 AGA
395628 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.24
8 1 0.04
9 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:396306 original size:30 final size:28
Alignment explanation
Indices: 396270--396380 Score: 82
Period size: 28 Copynumber: 3.8 Consensus size: 28
396260 TAAACTTAGC
396270 TAATTAATTACTAAAATATAATATAAAAAA
1 TAATTAATTA-TAAAA-ATAATATAAAAAA
* ****
396300 TAATTAATTATCAAAATAATAT-CCCCA
1 TAATTAATTATAAAAATAATATAAAAAA
*
396327 TCATATT-ATTGACCAAAATATAATATAAAAAA
1 T-A-ATTAATT-A-TAAAA-ATAATATAAAAAA
*
396359 TAATTAATTATGAAAATAATAT
1 TAATTAATTATAAAAATAATAT
396381 CCTCATCATA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
27 2 0.03
28 18 0.30
29 11 0.18
30 17 0.28
31 11 0.18
32 2 0.03
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (28 bp):
TAATTAATTATAAAAATAATATAAAAAA
Found at i:396345 original size:59 final size:59
Alignment explanation
Indices: 396282--396404 Score: 219
Period size: 59 Copynumber: 2.1 Consensus size: 59
396272 ATTAATTACT
396282 AAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGACC
1 AAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGACC
* * *
396341 AAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCTCATCATATTATTTACC
1 AAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGACC
396400 AAAAT
1 AAAAT
396405 GGTACAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (59 bp):
AAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGACC
Found at i:396798 original size:9 final size:9
Alignment explanation
Indices: 396784--396820 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
396774 TTTTTTTTCC
396784 TCTCCTTCT
1 TCTCCTTCT
396793 TCTCCTTCT
1 TCTCCTTCT
*
396802 CCTCCTTC-
1 TCTCCTTCT
396810 T-TCCTTCT
1 TCTCCTTCT
396818 TCT
1 TCT
396821 TTCTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.25
8 1 0.04
9 17 0.71
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (9 bp):
TCTCCTTCT
Found at i:396824 original size:4 final size:4
Alignment explanation
Indices: 396817--396859 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
396807 TTCTTCCTTC
*
396817 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
396860 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:396856 original size:11 final size:11
Alignment explanation
Indices: 396814--396870 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
396804 TCCTTCTTCC
*
396814 TTCTTCTTTCT
1 TTCTTTTTTCT
396825 TTCTTTCTTTCTT
1 TTCTTT-TTTC-T
396838 TCTCTTTTTTCT
1 T-TCTTTTTTCT
*
396850 TTCTTTTTTCC
1 TTCTTTTTTCT
*
396861 TTCATTTTTC
1 TTCTTTTTTC
396871 GTTGGTCCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 23 0.57
12 6 0.15
13 6 0.15
14 5 0.12
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:397119 original size:27 final size:27
Alignment explanation
Indices: 397042--397107 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
397032 ACACCCCTTA
397042 GTGCCGCCACTTGATATTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCATTG
397069 GTGCCGCCACTTGATATTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCATTG
397096 GTGCCGCCACTT
1 GTGCCGCCACTT
397108 AGTGTTCCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.14, C:0.35, G:0.20, T:0.32
Consensus pattern (27 bp):
GTGCCGCCACTTGATATTCCTCCATTG
Found at i:402845 original size:13 final size:14
Alignment explanation
Indices: 402827--402861 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
402817 TACACATAAA
402827 ATATGT-AAAATCC
1 ATATGTCAAAATCC
402840 ATATGTCCAAAATCC
1 ATATGT-CAAAATCC
402855 ATATGTC
1 ATATGTC
402862 CATCAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 1 0.05
15 13 0.65
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (14 bp):
ATATGTCAAAATCC
Found at i:402853 original size:15 final size:15
Alignment explanation
Indices: 402833--402863 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
402823 TAAAATATGT
402833 AAAATCCATATGTCC
1 AAAATCCATATGTCC
402848 AAAATCCATATGTCC
1 AAAATCCATATGTCC
402863 A
1 A
402864 TCAATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAATCCATATGTCC
Found at i:414294 original size:12 final size:12
Alignment explanation
Indices: 414264--414302 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
414254 AAAAAAAAAA
*
414264 ATATATATATAT
1 ATATATGTATAT
414276 ATATATGTATAT
1 ATATATGTATAT
* *
414288 GTATATGTACAT
1 ATATATGTATAT
414300 ATA
1 ATA
414303 CTCATTGCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:417192 original size:18 final size:19
Alignment explanation
Indices: 417146--417192 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
417136 ATTTATCTCA
417146 TAAAAAATTACACTAAATC
1 TAAAAAATTACACTAAATC
* * *
417165 T-AAGATTTACAC-AAATT
1 TAAAAAATTACACTAAATC
417182 TAAAAAATTAC
1 TAAAAAATTAC
417193 TATTTGGAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAAATTACACTAAATC
Done.