Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 174 of 195
Found at i:29125503 original size:12 final size:12
Alignment explanation
Indices: 29125488--29125513 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29125478 AGAGTTAAAC
29125488 AACAATTAGAGA
1 AACAATTAGAGA
29125500 AACAATTAGAGA
1 AACAATTAGAGA
29125512 AA
1 AA
29125514 TCTCACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (12 bp):
AACAATTAGAGA
Found at i:29130812 original size:74 final size:73
Alignment explanation
Indices: 29130705--29130860 Score: 204
Period size: 74 Copynumber: 2.1 Consensus size: 73
29130695 TTGTCCCGAG
** * * *
29130705 AAAAAGAAAACAAGTAAAATCAGAATAACATTAACAAATCCCTGCATTGTAAGCTACTTTCGGGC
1 AAAAA-AAAACAAGTAAAATCAGAATAACATTAACAAATCCCTGCATAATAAACTAATTTCAGGC
29130770 ATAAATAAT
65 ATAAATAAT
* * * * *
29130779 AATAAAAAAATAAGTGAAATCAGAATAATATTAACAAATCCCTGCGTAATAAACTAATTTCATGC
1 AA-AAAAAAACAAGTAAAATCAGAATAACATTAACAAATCCCTGCATAATAAACTAATTTCAGGC
29130844 ATAAATAAT
65 ATAAATAAT
29130853 AAAAAAAA
1 AAAAAAAA
29130861 TTAATGTCAC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
73 6 0.08
74 62 0.87
75 3 0.04
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (73 bp):
AAAAAAAAACAAGTAAAATCAGAATAACATTAACAAATCCCTGCATAATAAACTAATTTCAGGCA
TAAATAAT
Found at i:29131511 original size:16 final size:16
Alignment explanation
Indices: 29131492--29131523 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29131482 ATAAATGATT
*
29131492 AAATGATTAAATTCAA
1 AAATAATTAAATTCAA
29131508 AAATAATTAAATTCAA
1 AAATAATTAAATTCAA
29131524 TCAATTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (16 bp):
AAATAATTAAATTCAA
Found at i:29131660 original size:16 final size:17
Alignment explanation
Indices: 29131629--29131668 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
29131619 AATTGAGTTT
29131629 ATGAATATCATAAATTC
1 ATGAATATCATAAATTC
*
29131646 ATGAAT-TCTTAAATTC
1 ATGAATATCATAAATTC
*
29131662 ATAAATA
1 ATGAATA
29131669 ATCAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (17 bp):
ATGAATATCATAAATTC
Found at i:29131748 original size:74 final size:73
Alignment explanation
Indices: 29131599--29131752 Score: 159
Period size: 74 Copynumber: 2.1 Consensus size: 73
29131589 TGGAACGAAT
* * * * *
29131599 AATATAATTTATTTATAATTAATTGAGTTTATGAATATCATAAATTCATGAATTCTTAAATTCAT
1 AATAT-ATTTATTTATAATTAATTAAATTCATGAATATCATAAATTCATGAATACTTAAATTAAT
29131664 AAATAATCAA
65 AAATAATC-A
* * * *
29131674 AATATATTTATTTATAATTAATTAAATTCATTG-GTATTATAATTTCATGAATGAC-TAAGTTAA
1 AATATATTTATTTATAATTAATTAAATTCA-TGAATATCATAAATTCATGAAT-ACTTAAATTAA
* *
29131737 TGAATATTCA
64 TAAATAATCA
29131747 AATATA
1 AATATA
29131753 ATAAACTCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
73 7 0.11
74 51 0.77
75 8 0.12
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (73 bp):
AATATATTTATTTATAATTAATTAAATTCATGAATATCATAAATTCATGAATACTTAAATTAATA
AATAATCA
Found at i:29137327 original size:75 final size:75
Alignment explanation
Indices: 29137238--29137393 Score: 222
Period size: 75 Copynumber: 2.1 Consensus size: 75
29137228 CCCTTTCAAG
* * * * *
29137238 AAAAAGAAAGCAAGTAAAATCAGAATAACATTAACAAATCCCTGCATAGTAAGCTACTTTCAGGC
1 AAAAAAAAAACAAGTAAAATCAGAATAACATTAACAAATCCCTGCATAATAAACTAATTTCAGGC
29137303 ATAAATAATA
66 ATAAATAATA
* * * *
29137313 AAAAAAAAAACAAGTGAAATCAGAATAATATTAACAAGTCCCTGCATAATAAACTAATTTCATGC
1 AAAAAAAAAACAAGTAAAATCAGAATAACATTAACAAATCCCTGCATAATAAACTAATTTCAGGC
*
29137378 ATAAATACTA
66 ATAAATAATA
29137388 AAAAAA
1 AAAAAA
29137394 TTAATGTCAC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (75 bp):
AAAAAAAAAACAAGTAAAATCAGAATAACATTAACAAATCCCTGCATAATAAACTAATTTCAGGC
ATAAATAATA
Found at i:29138040 original size:16 final size:16
Alignment explanation
Indices: 29138021--29138052 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29138011 ATAAATGATT
*
29138021 AAATGATTAAATTCAA
1 AAATAATTAAATTCAA
29138037 AAATAATTAAATTCAA
1 AAATAATTAAATTCAA
29138053 TCAATTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (16 bp):
AAATAATTAAATTCAA
Found at i:29138194 original size:16 final size:17
Alignment explanation
Indices: 29138163--29138202 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
29138153 AATTGAGTTT
29138163 ATGAATATCATAAATTC
1 ATGAATATCATAAATTC
*
29138180 ATGAAT-TCTTAAATTC
1 ATGAATATCATAAATTC
*
29138196 ATAAATA
1 ATGAATA
29138203 ATCAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (17 bp):
ATGAATATCATAAATTC
Found at i:29138282 original size:74 final size:73
Alignment explanation
Indices: 29138133--29138286 Score: 159
Period size: 74 Copynumber: 2.1 Consensus size: 73
29138123 TGGAACGAAT
* * * * *
29138133 AATATAATTTATTTATAATTAATTGAGTTTATGAATATCATAAATTCATGAATTCTTAAATTCAT
1 AATAT-ATTTATTTATAATTAATTAAATTCATGAATATCATAAATTCATGAATACTTAAATTAAT
29138198 AAATAATCAA
65 AAATAATC-A
* * * *
29138208 AATATATTTATTTATAATTAATTAAATTCATTG-GTATTATAATTTCATGAATGAC-TAAGTTAA
1 AATATATTTATTTATAATTAATTAAATTCA-TGAATATCATAAATTCATGAAT-ACTTAAATTAA
* *
29138271 TGAATATTCA
64 TAAATAATCA
29138281 AATATA
1 AATATA
29138287 ATAAACTCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
73 7 0.11
74 51 0.77
75 8 0.12
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (73 bp):
AATATATTTATTTATAATTAATTAAATTCATGAATATCATAAATTCATGAATACTTAAATTAATA
AATAATCA
Found at i:29140492 original size:2 final size:2
Alignment explanation
Indices: 29140485--29140523 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
29140475 CCTTTTAGTT
*
29140485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29140524 GAGTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29145413 original size:16 final size:16
Alignment explanation
Indices: 29145358--29145404 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
29145348 GTTTTAAATT
29145358 AAGATTTTAGAGTTTC
1 AAGATTTTAGAGTTTC
29145374 AAGATTTTAGAGTTTC
1 AAGATTTTAGAGTTTC
* *
29145390 GAGATTTTAAAGTTT
1 AAGATTTTAGAGTTT
29145405 TAAGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (16 bp):
AAGATTTTAGAGTTTC
Found at i:29145901 original size:20 final size:20
Alignment explanation
Indices: 29145876--29145913 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29145866 CACTTCAATG
* *
29145876 AAAATTATTTTTATTATTGT
1 AAAATTACTATTATTATTGT
29145896 AAAATTACTATTATTATT
1 AAAATTACTATTATTATT
29145914 TGTTAAAAAT
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:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
AAAATTACTATTATTATTGT
Found at i:29145927 original size:21 final size:20
Alignment explanation
Indices: 29145886--29145930 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
29145876 AAAATTATTT
*
29145886 TTATTATTGTAAAATTACTA
1 TTATTATTGTAAAAATACTA
29145906 TTATTATTTGTTAAAAAT-CTA
1 TTATTA-TTG-TAAAAATACTA
29145927 TTAT
1 TTAT
29145931 CATTATCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 10 0.45
22 6 0.27
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (20 bp):
TTATTATTGTAAAAATACTA
Found at i:29157783 original size:3 final size:3
Alignment explanation
Indices: 29157775--29157833 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
29157765 GAAATCATTT
* * * *
29157775 TTA TTA TTA TTG TTG TTG TTA TTA TTA TTA TTA TTG TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
29157824 TCA TTA TTA T
1 TTA TTA TTA T
29157834 GAAACAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 47 0.96
4 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:29157798 original size:18 final size:18
Alignment explanation
Indices: 29157775--29157822 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
29157765 GAAATCATTT
* *
29157775 TTATTATTATTGTTGTTG
1 TTATTATTATTATTATTG
29157793 TTATTATTATTATTATTG
1 TTATTATTATTATTATTG
29157811 TTATTATTATTA
1 TTATTATTATTA
29157823 ATCATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TTATTATTATTATTATTG
Found at i:29159562 original size:22 final size:23
Alignment explanation
Indices: 29159491--29159611 Score: 119
Period size: 23 Copynumber: 5.4 Consensus size: 23
29159481 CTACAAATCG
* *
29159491 AAATTATGCCTAGAGGTATT--A
1 AAATTATGCTTAGAGGTCTTAGA
**
29159512 AAATTATG-TCCGAAGGTCTTAGA
1 AAATTATGCTTAG-AGGTCTTAGA
*
29159535 AAATTATACTTAGAGGTCTTA-A
1 AAATTATGCTTAGAGGTCTTAGA
29159557 AAATTATGCTT-GAAGGTCTTAGA
1 AAATTATGCTTAG-AGGTCTTAGA
*
29159580 AAATTATGCTCAGAGGTCTTA-A
1 AAATTATGCTTAGAGGTCTTAGA
*
29159602 AGATTATGCT
1 AAATTATGCT
29159612 CGAAGGTCTT
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.01
21 15 0.18
22 29 0.35
23 35 0.42
24 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (23 bp):
AAATTATGCTTAGAGGTCTTAGA
Found at i:29159575 original size:45 final size:45
Alignment explanation
Indices: 29159491--29159622 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 45
29159481 CTACAAATCG
* *
29159491 AAATTATGCCTAGAGGTATT-AAAATTATG-TCCGAAGGTCTTAGA
1 AAATTATGCTTAGAGGTCTTAAAAATTATGCT-CGAAGGTCTTAGA
* *
29159535 AAATTATACTTAGAGGTCTTAAAAATTATGCTTGAAGGTCTTAGA
1 AAATTATGCTTAGAGGTCTTAAAAATTATGCTCGAAGGTCTTAGA
* *
29159580 AAATTATGCTCAGAGGTCTTAAAGATTATGCTCGAAGGTCTTA
1 AAATTATGCTTAGAGGTCTTAAAAATTATGCTCGAAGGTCTTA
29159623 CAAATCTCAG
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
44 17 0.22
45 60 0.77
46 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (45 bp):
AAATTATGCTTAGAGGTCTTAAAAATTATGCTCGAAGGTCTTAGA
Found at i:29159612 original size:22 final size:23
Alignment explanation
Indices: 29159491--29159627 Score: 128
Period size: 22 Copynumber: 6.2 Consensus size: 23
29159481 CTACAAATCG
*
29159491 AAATTATGC-CTAG-AGGTATT-A
1 AAATTATGCTC-AGAAGGTCTTAA
*
29159512 AAATTATG-TCCGAAGGTCTTAGA
1 AAATTATGCTCAGAAGGTCTTA-A
* *
29159535 AAATTATACTTAG-AGGTCTTAA
1 AAATTATGCTCAGAAGGTCTTAA
*
29159557 AAATTATGCT-TGAAGGTCTTAGA
1 AAATTATGCTCAGAAGGTCTTA-A
29159580 AAATTATGCTCAG-AGGTCTTAA
1 AAATTATGCTCAGAAGGTCTTAA
* *
29159602 AGATTATGCTC-GAAGGTCTTAC
1 AAATTATGCTCAGAAGGTCTTAA
29159624 AAAT
1 AAAT
29159628 CTCAGAATCT
Statistics
Matches: 96, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.01
21 17 0.18
22 40 0.42
23 35 0.36
24 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
AAATTATGCTCAGAAGGTCTTAA
Found at i:29159747 original size:23 final size:23
Alignment explanation
Indices: 29159694--29159755 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
29159684 AAATCTTTTA
*
29159694 CCCGAAGGTC-TTAAAAATTCTG
1 CCCGAAGGTCTTTAAAAATTATG
* *
29159716 CCTCG-AGGTCTTTAGAGATTATG
1 CC-CGAAGGTCTTTAAAAATTATG
29159739 CCCGAAGGTCTTATAAA
1 CCCGAAGGTCTT-TAAA
29159756 TCTCAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 9 0.28
23 20 0.62
24 3 0.09
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
CCCGAAGGTCTTTAAAAATTATG
Found at i:29159798 original size:129 final size:128
Alignment explanation
Indices: 29159568--29159841 Score: 390
Period size: 129 Copynumber: 2.1 Consensus size: 128
29159558 AATTATGCTT
* *
29159568 GAAGGTCTTAGAAAATTATGCTCAGAGGTCTTAAAGATTATGCTCGAAGGTCTTACAAATCTCAG
1 GAAGGTCTTA-AAAATTATGCTCAGAGGTCTTAAAGATTATGCCCGAAGGTCTTACAAATCTCAA
* * *
29159633 AATCTTTGAATGCTCCTTCTGATCAAAGGTAATGAAACTTTGAAAATTTAAAAATCTTTTACCC
65 AATCTTTGAATGCTCCTTCTGATCAAAGGCAATGAAACTTTAAAAATGTAAAAATCTTTTACCC
* * *
29159697 GAAGGTCTTAAAAATTCTGCCTC-GAGGTCTTTAGAGATTATGCCCGAAGGTCTTATAAATCTCA
1 GAAGGTCTTAAAAATTATG-CTCAGAGGTC-TTAAAGATTATGCCCGAAGGTCTTACAAATCTCA
**
29159761 AAATCTTTGAATG-TTTTTCTCGATCAAAGGCAATGAAACTTTAAAAATGTAAAAATCTTTTACC
64 AAATCTTTGAATGCTCCTTCT-GATCAAAGGCAATGAAACTTTAAAAATGTAAAAATCTTTTACC
29159825 C
128 C
* *
29159826 AAAGATCTTAAAAATT
1 GAAGGTCTTAAAAATT
29159842 GTATCTGAAG
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
128 19 0.15
129 111 0.85
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (128 bp):
GAAGGTCTTAAAAATTATGCTCAGAGGTCTTAAAGATTATGCCCGAAGGTCTTACAAATCTCAAA
ATCTTTGAATGCTCCTTCTGATCAAAGGCAATGAAACTTTAAAAATGTAAAAATCTTTTACCC
Found at i:29159859 original size:129 final size:129
Alignment explanation
Indices: 29159602--29159880 Score: 382
Period size: 129 Copynumber: 2.2 Consensus size: 129
29159592 GAGGTCTTAA
* *
29159602 AGATTATGCTCGAAGGTCTTACAAATCTCAGAATCTTTGAATGCTCCTTCTGATCAAAGGTAATG
1 AGATTATGCTCGAAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTTCTGATCAAAGGCAATG
* * * * * *
29159667 AAACTTTGAAAATTTAAAAATCTTTTACCCGAAGGTCTTAAAAATTCTGCCTCGAGGTCTTTAG
66 AAACTTTAAAAATGTAAAAATCTTTTACCCAAAGATCTTAAAAATTCTACCTCGAGGTATTTAG
* * **
29159731 AGATTATGCCCGAAGGTCTTATAAATCTCAAAATCTTTGAATG-TTTTTCTCGATCAAAGGCAAT
1 AGATTATGCTCGAAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTTCT-GATCAAAGGCAAT
* *
29159795 GAAACTTTAAAAATGTAAAAATCTTTTACCCAAAGATCTTAAAAATTGTATCT-GAAGGTATTTA
65 GAAACTTTAAAAATGTAAAAATCTTTTACCCAAAGATCTTAAAAATTCTACCTCG-AGGTATTTA
29159859 G
129 G
* *
29159860 AGATTGTGCTCAAAGGTCTTA
1 AGATTATGCTCGAAGGTCTTA
29159881 GAGATTATGT
Statistics
Matches: 131, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
128 6 0.05
129 125 0.95
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (129 bp):
AGATTATGCTCGAAGGTCTTACAAATCTCAAAATCTTTGAATGCTCCTTCTGATCAAAGGCAATG
AAACTTTAAAAATGTAAAAATCTTTTACCCAAAGATCTTAAAAATTCTACCTCGAGGTATTTAG
Found at i:29159897 original size:22 final size:22
Alignment explanation
Indices: 29159845--29159901 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
29159835 AAAAATTGTA
* *
29159845 TCTGAAGGTATTTAGAGATTGTG
1 TCTGAAGGT-CTTAGAGATTATG
*
29159868 -CTCAAAGGTCTTAGAGATTATG
1 TCT-GAAGGTCTTAGAGATTATG
29159890 TCTGAAGGTCTT
1 TCTGAAGGTCTT
29159902 GAAAATTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (22 bp):
TCTGAAGGTCTTAGAGATTATG
Found at i:29160012 original size:21 final size:22
Alignment explanation
Indices: 29159972--29160027 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
29159962 TTACCCAAAA
29159972 GTCTTAAAAATTATGCCCAGAG
1 GTCTTAAAAATTATGCCCAGAG
29159994 GTCTTAAAAATTATG-CCAGAG
1 GTCTTAAAAATTATGCCCAGAG
*
29160015 GTCTGAAAAATTA
1 GTCTTAAAAATTA
29160028 CAAAATCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (22 bp):
GTCTTAAAAATTATGCCCAGAG
Found at i:29160055 original size:118 final size:118
Alignment explanation
Indices: 29159895--29160107 Score: 286
Period size: 118 Copynumber: 1.8 Consensus size: 118
29159885 TTATGTCTGA
* *
29159895 AGGTCTTGAAAATTACAAAATCTTTGAATACTCCTCTTAATCAAAGACAATGAAACATTAAAATG
1 AGGTCTTGAAAATTACAAAATCTTTGAATACTCATCTTAATCAAAGACAATGAAACATTAAAATA
29159960 TTTTACCCAAAAGTCTTAAAAATTATGCCCAGAGGTCTTAAAAATTATGCCAG
66 TTTTACCCAAAAGTCTTAAAAATTATGCCCAGAGGTCTTAAAAATTATGCCAG
* * ** *
29160013 AGGTC-TGAAAAATTACAAAATCTTTGAATGCTCAT-TTCAATCAGAGGTAATGAAACTTTAAAA
1 AGGTCTTG-AAAATTACAAAATCTTTGAATACTCATCTT-AATCAAAGACAATGAAACATTAAAA
*** * *
29160076 TATTTTACCTTGAGGTCTTGAAAATTATGCCC
64 TATTTTACCCAAAAGTCTTAAAAATTATGCCC
29160108 GAAAGTCTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
117 4 0.05
118 77 0.95
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (118 bp):
AGGTCTTGAAAATTACAAAATCTTTGAATACTCATCTTAATCAAAGACAATGAAACATTAAAATA
TTTTACCCAAAAGTCTTAAAAATTATGCCCAGAGGTCTTAAAAATTATGCCAG
Found at i:29160140 original size:97 final size:94
Alignment explanation
Indices: 29159991--29160269 Score: 290
Period size: 97 Copynumber: 2.9 Consensus size: 94
29159981 ATTATGCCCA
* * *
29159991 GAGGTCTTAAAAATTATGCCAGAGGTCTGAAAAATTACAAAATCTTTGAATGCTCATTTCAATCA
1 GAGGTCTTGAAAATTATGCCAGAGGTCT-TAAAATTACAAAATCTTTGAATGCTCATCTCAATCA
*
29160056 GAGGTAATGAAACTTTAAAATATTTTACCTT
65 GAGGTAATGAAACTTTAAAATATTTTACC-C
* * ** * * * *
29160087 GAGGTCTTGAAAATTATGCCCGAAAGTCTTACAAATTTTAAAATCTTTAAATGCTCCTCCCAATA
1 GAGGTCTTGAAAATTATGCCAG-AGGTCTTA-AAATTACAAAATCTTTGAATGCTCATCTCAATC
* ** *
29160152 AGAGGTAATGAAACTTCAAAACGTTTTGCCC
64 AGAGGTAATGAAACTTTAAAATATTTTACCC
* * **
29160183 AAGGGTCTTGAAAATTATACTTTGAGGTCTTAAATATTACAAAATCTTTGAATGCTCATCT-AAT
1 GA-GGTCTTGAAAATTATGC-CAGAGGTCTTAAA-ATTACAAAATCTTTGAATGCTCATCTCAAT
* *
29160247 CAGAGGCAACGAAACTTTAAAAT
63 CAGAGGTAATGAAACTTTAAAAT
29160270 TTTAAAATTT
Statistics
Matches: 147, Mismatches: 31, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
96 45 0.31
97 101 0.69
98 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (94 bp):
GAGGTCTTGAAAATTATGCCAGAGGTCTTAAAATTACAAAATCTTTGAATGCTCATCTCAATCAG
AGGTAATGAAACTTTAAAATATTTTACCC
Found at i:29161460 original size:38 final size:37
Alignment explanation
Indices: 29161400--29161471 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
29161390 ATCGATATGG
*
29161400 ATGGGATGAAATGCTCATATTATCATATTATGATGCAC
1 ATGGGATGAAATACTCATATTATCATATTA-GATGCAC
* *
29161438 ATGGGATGAAATACATGA-ATTATCTTATTAGATG
1 ATGGGATGAAATAC-TCATATTATCATATTAGATG
29161472 TATAAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 4 0.13
38 24 0.80
39 2 0.07
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (37 bp):
ATGGGATGAAATACTCATATTATCATATTAGATGCAC
Found at i:29163460 original size:14 final size:14
Alignment explanation
Indices: 29163438--29163506 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
29163428 GGGTGTGGGA
*
29163438 TTTTGGATTTTAGG
1 TTTTTGATTTTAGG
* *
29163452 TTTTTGATTTTTGA
1 TTTTTGATTTTAGG
29163466 TTTTTGAGTTTTGAGG
1 TTTTTGA-TTTT-AGG
**
29163482 TTTGAGATTTTA-G
1 TTTTTGATTTTAGG
29163495 -TTTTGATTTTAG
1 TTTTTGATTTTAG
29163507 AAGGTTTAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
12 9 0.21
13 1 0.02
14 19 0.44
15 8 0.19
16 6 0.14
ACGTcount: A:0.16, C:0.00, G:0.23, T:0.61
Consensus pattern (14 bp):
TTTTTGATTTTAGG
Found at i:29163462 original size:21 final size:20
Alignment explanation
Indices: 29163416--29163504 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 20
29163406 GATTTAAAGG
**
29163416 TTTTGGATTTTAGGGTGTGGGA
1 TTTTGGATTTTA-GGT-TTTGA
29163438 TTTTGGATTTTAGGTTTTTGA
1 TTTTGGATTTTAGG-TTTTGA
* *
29163459 TTTTTGATTTTTGAGTTTTGA
1 TTTTGGATTTTAG-GTTTTGA
*
29163480 GGTTTGAGATTTTA-GTTTTGA
1 -TTTTG-GATTTTAGGTTTTGA
29163501 TTTT
1 TTTT
29163505 AGAAGGTTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.05
21 29 0.53
22 17 0.31
23 6 0.11
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (20 bp):
TTTTGGATTTTAGGTTTTGA
Found at i:29163470 original size:7 final size:7
Alignment explanation
Indices: 29163436--29163479 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
29163426 TAGGGTGTGG
*
29163436 GATTTTG
1 GATTTTT
*
29163443 GATTTTA
1 GATTTTT
*
29163450 GGTTTTT
1 GATTTTT
29163457 GATTTTT
1 GATTTTT
29163464 GATTTTT
1 GATTTTT
*
29163471 GAGTTTT
1 GATTTTT
29163478 GA
1 GA
29163480 GGTTTGAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.23, T:0.61
Consensus pattern (7 bp):
GATTTTT
Found at i:29163480 original size:7 final size:7
Alignment explanation
Indices: 29163453--29163504 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
29163443 GATTTTAGGT
*
29163453 TTTTGAT
1 TTTTGAG
*
29163460 TTTTGAT
1 TTTTGAG
29163467 TTTTGAG
1 TTTTGAG
29163474 TTTTGAG
1 TTTTGAG
*
29163481 GTTTGAG
1 TTTTGAG
29163488 ATTTT-AG
1 -TTTTGAG
29163495 TTTTGA-
1 TTTTGAG
29163501 TTTT
1 TTTT
29163505 AGAAGGTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
6 8 0.20
7 29 0.73
8 3 0.08
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.63
Consensus pattern (7 bp):
TTTTGAG
Found at i:29163952 original size:3 final size:3
Alignment explanation
Indices: 29163946--29163986 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
29163936 ATTATAGTTG
* *
29163946 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTAA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA T
29163987 GAAACAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29163957 original size:18 final size:18
Alignment explanation
Indices: 29163934--29163975 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
29163924 GAAATCATTT
29163934 TTATTA-TAGTTGTTATTA
1 TTATTATTA-TTGTTATTA
29163952 TTATTATTATTGTTATTA
1 TTATTATTATTGTTATTA
29163970 TTATTA
1 TTATTA
29163976 ATCATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (18 bp):
TTATTATTATTGTTATTA
Found at i:29164062 original size:33 final size:32
Alignment explanation
Indices: 29164025--29164096 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
29164015 TCTAAAAGTT
29164025 TTAAAATATG-CATAAATAACA-ATAATAATAAAA
1 TTAAAA-ATGACATAAATAACATATAA-AA-AAAA
* *
29164058 TTAAAAATGATATAAATAATATATAAAAAAAA
1 TTAAAAATGACATAAATAACATATAAAAAAAA
29164090 TTAAAAA
1 TTAAAAA
29164097 AAATTTTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 14 0.40
33 17 0.49
34 4 0.11
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (32 bp):
TTAAAAATGACATAAATAACATATAAAAAAAA
Found at i:29164737 original size:15 final size:16
Alignment explanation
Indices: 29164705--29164746 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
29164695 CGGGGAAATT
*
29164705 TTTTTTTTTGTATATC
1 TTTTTGTTTGTATATC
*
29164721 TTTTTGTTTGT-TTTC
1 TTTTTGTTTGTATATC
*
29164736 TTTTTGGTTGT
1 TTTTTGTTTGT
29164747 GGCTAGATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.05, C:0.05, G:0.14, T:0.76
Consensus pattern (16 bp):
TTTTTGTTTGTATATC
Found at i:29165161 original size:33 final size:31
Alignment explanation
Indices: 29165121--29165189 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
29165111 GTTTTTGCTC
29165121 TTTTTGTTTTTTTATCT-TATTGTTTATTT-TATT
1 TTTTTG-TTTTTT-TCTAT-TTGTTT-TTTGTATT
29165154 TTTTTGTTTTTTTCTATTTGTTTTTTGTATT
1 TTTTTGTTTTTTTCTATTTGTTTTTTGTATT
29165185 TTTTT
1 TTTTT
29165190 AATATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 3 0.09
31 18 0.53
32 7 0.21
33 6 0.18
ACGTcount: A:0.09, C:0.03, G:0.07, T:0.81
Consensus pattern (31 bp):
TTTTTGTTTTTTTCTATTTGTTTTTTGTATT
Found at i:29165164 original size:31 final size:30
Alignment explanation
Indices: 29165112--29165189 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
29165102 AGCCCCCTGG
*
29165112 TTTTTGCTCTTTTTGTTTTTTTATCT-TATTGT
1 TTTTTG-TATTTTT-TTTTTTTATCTAT-TTGT
*
29165144 TTATTT-TATTTTTTTGTTTTTTTCTATTTGT
1 TT-TTTGTATTTTTTT-TTTTTATCTATTTGT
29165175 TTTTTGTATTTTTTT
1 TTTTTGTATTTTTTT
29165190 AATATTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
30 5 0.12
31 29 0.73
32 3 0.08
33 3 0.08
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.79
Consensus pattern (30 bp):
TTTTTGTATTTTTTTTTTTTATCTATTTGT
Found at i:29166186 original size:33 final size:33
Alignment explanation
Indices: 29166145--29166218 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
29166135 CAATTGTCGG
*
29166145 ATAAAATATCAATGCTCATCTCTATTGTGTGTC
1 ATAAAATATAAATGCTCATCTCTATTGTGTGTC
*
29166178 ATAGAATATAAATGCTCATCTCTATTGTGTGTC
1 ATAAAATATAAATGCTCATCTCTATTGTGTGTC
29166211 ATAAAATA
1 ATAAAATA
29166219 CGATCCCCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (33 bp):
ATAAAATATAAATGCTCATCTCTATTGTGTGTC
Found at i:29166829 original size:39 final size:39
Alignment explanation
Indices: 29166765--29166842 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
29166755 CCACGTAAGC
* * *
29166765 AGCCCTCCTTTATACAAATCTGTTCAATAATTAGATTGT
1 AGCCATCCTTTATAAAAATCAGTTCAATAATTAGATTGT
29166804 AGCCATCCTTTATAAAAATCAGTTCAATAATTAGATTGT
1 AGCCATCCTTTATAAAAATCAGTTCAATAATTAGATTGT
29166843 TTGTATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (39 bp):
AGCCATCCTTTATAAAAATCAGTTCAATAATTAGATTGT
Found at i:29167168 original size:21 final size:20
Alignment explanation
Indices: 29167138--29167179 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
29167128 TTAAAATATT
29167138 TAATTTTTTAATTCAATCTA
1 TAATTTTTTAATTCAATCTA
*
29167158 TAATATTTTTAATTTAATCTA
1 TAAT-TTTTTAATTCAATCTA
29167179 T
1 T
29167180 CACTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATTTTTTAATTCAATCTA
Found at i:29169109 original size:62 final size:62
Alignment explanation
Indices: 29168868--29169282 Score: 263
Period size: 62 Copynumber: 6.7 Consensus size: 62
29168858 GGGAAAATAT
* ** * * * * * * * *
29168868 GATTATTGAAGGTGTTTTTGACTAAAAATGCCTCCAATAATCCCCTTCAATTTTTTTTTA-G
1 GATTATTGAAGGTATTTCAGGCAAAAAATACCTTCAATAATCTCTTTCAATTTTTTATAAGG
* * ** * * * *
29168929 GATTATTCAAGATATTTCTA-AAAAAAAAAACCTTCAATAATC-CTCTCCATTTTTTATGAGGG
1 GATTATTGAAGGTATTTC-AGGCAAAAAATACCTTCAATAATCTCTTTCAATTTTTTAT-AAGG
* * ** * * * ** *
29168991 GATTATTGAAGACGT-TTTCTGTCAAAAAACGCATTCAATAGTCCCAAAT-ACTTTTTTATAAGG
1 GATTATTGAAG--GTATTTCAGGCAAAAAATACCTTCAATAATCTC-TTTCAATTTTTTATAAGG
* * *
29169054 GATTATTGAAGGTATTTCAGGCAAAAAATACATTCAATAATCTCTTTCAATTTTTTA-CAGAA
1 GATTATTGAAGGTATTTCAGGCAAAAAATACCTTCAATAATCTCTTTCAATTTTTTATAAG-G
* * * ** * * *
29169116 GATTATTGAATGTATTTTCTGTC-AAAAACGCCTTTAAAAATCTCTTTC-ATTTTTTATAAAG
1 GATTATTGAAGGTA-TTTCAGGCAAAAAATACCTTCAATAATCTCTTTCAATTTTTTATAAGG
** * * *
29169177 GATTATTGAAGGCGTTTTAGGCAAAAAAATACCTTCAATAATCTC-TTCTAATTTTTTATGAGA
1 GATTATTGAAGGTATTTCAGGC-AAAAAATACCTTCAATAATCTCTTTC-AATTTTTTATAAGG
* *
29169240 GATTATTGAAGGTGTTTCAGGCAAAAAATACCTTGAATAATCT
1 GATTATTGAAGGTATTTCAGGCAAAAAATACCTTCAATAATCT
29169283 GCTTATAAAA
Statistics
Matches: 269, Mismatches: 68, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
60 16 0.06
61 58 0.22
62 114 0.42
63 70 0.26
64 10 0.04
65 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (62 bp):
GATTATTGAAGGTATTTCAGGCAAAAAATACCTTCAATAATCTCTTTCAATTTTTTATAAGG
Found at i:29169267 original size:124 final size:123
Alignment explanation
Indices: 29169042--29169266 Score: 312
Period size: 123 Copynumber: 1.8 Consensus size: 123
29169032 TCCCAAATAC
* *
29169042 TTTTTTATAAGGGATTATTGAAGGTATTTCAGGCAAAAAATACATTCAATAATCTCTTTCAATTT
1 TTTTTTATAAAGGATTATTGAAGGCATTTCAGGCAAAAAATACATTCAATAATCTCTTTCAATTT
* * * *
29169107 TTTACAGAAGATTATTGAATGTATTTTCTGTCAAAAACGCCTTTAAAAATCTCTTTCA
66 TTTACAGAAGATTATTGAAGGTAGTTTCAGGCAAAAACGCCTTTAAAAATCTCTTTCA
* * *
29169165 TTTTTTATAAAGGATTATTGAAGGCGTTTTAGGCAAAAAAATACCTTCAATAATCTC-TTCTAAT
1 TTTTTTATAAAGGATTATTGAAGGCATTTCAGGC-AAAAAATACATTCAATAATCTCTTTC-AAT
*
29169229 TTTTTA-TGAGAGATTATTGAAGGT-GTTTCAGGCAAAAA
64 TTTTTACAGA-AGATTATTGAAGGTAGTTTCAGGCAAAAA
29169267 ATACCTTGAA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
123 46 0.52
124 43 0.48
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (123 bp):
TTTTTTATAAAGGATTATTGAAGGCATTTCAGGCAAAAAATACATTCAATAATCTCTTTCAATTT
TTTACAGAAGATTATTGAAGGTAGTTTCAGGCAAAAACGCCTTTAAAAATCTCTTTCA
Found at i:29169282 original size:124 final size:123
Alignment explanation
Indices: 29169042--29169282 Score: 299
Period size: 124 Copynumber: 2.0 Consensus size: 123
29169032 TCCCAAATAC
* *
29169042 TTTTTTATAAGGGATTATTGAAGGTATTTCAGGCAAAAAATACATTCAATAATCTCTTTCAATTT
1 TTTTTTATAAAGGATTATTGAAGGCATTTCAGGCAAAAAATACATTCAATAATCTCTTTCAATTT
* * * * * *
29169107 TTTACAGAAGATTATTGAATGTATTTTCTGTCAAAAACGCCTTTAAAAATCTCTTTCA
66 TTTACAGAAGATTATTGAAGGTAGTTTCAGGCAAAAACACCTTGAAAAATCTCTTTCA
* * *
29169165 TTTTTTATAAAGGATTATTGAAGGCGTTTTAGGCAAAAAAATACCTTCAATAATCTC-TTCTAAT
1 TTTTTTATAAAGGATTATTGAAGGCATTTCAGGC-AAAAAATACATTCAATAATCTCTTTC-AAT
* * *
29169229 TTTTTA-TGAGAGATTATTGAAGGT-GTTTCAGGCAAAAAATACCTTGAATAATCT
64 TTTTTACAGA-AGATTATTGAAGGTAGTTTCAGGC-AAAAACACCTTGAAAAATCT
29169283 GCTTATAAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
123 41 0.41
124 59 0.59
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (123 bp):
TTTTTTATAAAGGATTATTGAAGGCATTTCAGGCAAAAAATACATTCAATAATCTCTTTCAATTT
TTTACAGAAGATTATTGAAGGTAGTTTCAGGCAAAAACACCTTGAAAAATCTCTTTCA
Found at i:29169306 original size:62 final size:63
Alignment explanation
Indices: 29169177--29169318 Score: 164
Period size: 62 Copynumber: 2.3 Consensus size: 63
29169167 TTTTATAAAG
* * ****
29169177 GATTATTGAAGGCGTTTTAGGCAAAAAAATACCTTCAATAATCTCTTCTAATTTTTTATGAGA
1 GATTATTGAAGGCGTTTCAGGCAAAAAAATACCTTCAATAATCTCTTATAATAAAATATGAGA
* * *
29169240 GATTATTGAAGGTGTTTCAGGC-AAAAAATACCTTGAATAATCTGCTTATAA-AAAATA-GAGGC
1 GATTATTGAAGGCGTTTCAGGCAAAAAAATACCTTCAATAATCT-CTTATAATAAAATATGA-GA
29169302 GATTATTGAAGGCGTTT
1 GATTATTGAAGGCGTTT
29169319 TCTGTCAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
61 2 0.03
62 39 0.58
63 26 0.39
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (63 bp):
GATTATTGAAGGCGTTTCAGGCAAAAAAATACCTTCAATAATCTCTTATAATAAAATATGAGA
Found at i:29169617 original size:64 final size:64
Alignment explanation
Indices: 29169509--29169631 Score: 142
Period size: 64 Copynumber: 1.9 Consensus size: 64
29169499 AATAATCAAC
* * *
29169509 TTTATTTTTTGTAAGGAGATTATTCAAAGTGTTGTCTACCAAAAATA-CCTTCAATAATCTCCTA
1 TTTATTTTTTATAAGGAGATTATTCAAAGTATTGTCTA-CAAAAAAAGCCTTCAATAATCTCCTA
* * * * *
29169573 TTTATTTTTTATGAGGGGATTATTC-AAGATATTTTTTACAAAAAAAGCTTTCAATAATC
1 TTTATTTTTTATAAGGAGATTATTCAAAG-TATTGTCTACAAAAAAAGCCTTCAATAATC
29169632 ACTTTAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
63 10 0.20
64 39 0.80
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (64 bp):
TTTATTTTTTATAAGGAGATTATTCAAAGTATTGTCTACAAAAAAAGCCTTCAATAATCTCCTA
Found at i:29170926 original size:18 final size:19
Alignment explanation
Indices: 29170903--29170938 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29170893 AAACAAATAG
*
29170903 ATTCAA-TTTTTTTTTTAC
1 ATTCAACTTTTTTATTTAC
29170921 ATTCAACTTTTTTATTTA
1 ATTCAACTTTTTTATTTA
29170939 TCTTATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTCAACTTTTTTATTTAC
Found at i:29181048 original size:36 final size:36
Alignment explanation
Indices: 29180984--29181055 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
29180974 TGAAAACTTA
*
29180984 AAAAAATTCAAACAATTTCAAAATTTTAATA-AAAT
1 AAAAAATTCAAAAAATTTCAAAATTTTAATATAAAT
*
29181019 AAAAAATTCAAAAAGATTTTGAAAA-TTTAATATAAAT
1 AAAAAATTCAAAAA-A-TTTCAAAATTTTAATATAAAT
29181056 GAGAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 13 0.41
36 8 0.25
37 11 0.34
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.32
Consensus pattern (36 bp):
AAAAAATTCAAAAAATTTCAAAATTTTAATATAAAT
Found at i:29181318 original size:19 final size:20
Alignment explanation
Indices: 29181296--29181342 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29181286 TATTTTTATG
*
29181296 AAAATTTTTTA-ATATTTTA
1 AAAATTTTTCAGATATTTTA
* *
29181315 AAAATATTTCAGATTTTTTA
1 AAAATTTTTCAGATATTTTA
29181335 AAAATTTT
1 AAAATTTT
29181343 AAGTTTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AAAATTTTTCAGATATTTTA
Found at i:29181432 original size:9 final size:10
Alignment explanation
Indices: 29181412--29181437 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29181402 AGATTTTTTT
29181412 AATTTTCAAA
1 AATTTTCAAA
29181422 AATTTTCAAA
1 AATTTTCAAA
29181432 AATTTT
1 AATTTT
29181438 AGATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (10 bp):
AATTTTCAAA
Found at i:29183352 original size:2 final size:2
Alignment explanation
Indices: 29183345--29183390 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
29183335 CTCGCTCACC
29183345 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29183387 CT CT
1 CT CT
29183391 TACTTTGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29183444 original size:16 final size:17
Alignment explanation
Indices: 29183417--29183450 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29183407 TGGATTGGGA
29183417 TTAATAATTTTAAAATG
1 TTAATAATTTTAAAATG
*
29183434 TTAAT-ATTTTAATATG
1 TTAATAATTTTAAAATG
29183450 T
1 T
29183451 GTCAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTAATAATTTTAAAATG
Found at i:29184114 original size:32 final size:31
Alignment explanation
Indices: 29184063--29184150 Score: 79
Period size: 32 Copynumber: 2.8 Consensus size: 31
29184053 GATTAGAAGA
* * *
29184063 AAATAATATAAAAAATAAAAAATTAATATCAT
1 AAATAATTTTAAAATTAAAAAATTAATAT-AT
* *
29184095 AAATAATTTTAAAATTAAAATA-TAATATTT
1 AAATAATTTTAAAATTAAAAAATTAATATAT
* *
29184125 AATATAATATTTAAATTTTAAAAATT
1 AA-ATAAT-TTTAAAATTAAAAAATT
29184151 TTTAATGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
30 3 0.07
31 11 0.24
32 30 0.67
33 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATAATTTTAAAATTAAAAAATTAATATAT
Found at i:29184121 original size:31 final size:31
Alignment explanation
Indices: 29184081--29184139 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
29184071 TAAAAAATAA
29184081 AAAATTAATATCATAA-ATAAT-TTTAAAATT
1 AAAATTAATAT-ATAATATAATATTTAAAATT
*
29184111 AAAATATAATATTTAATATAATATTTAAA
1 AAAAT-TAATATATAATATAATATTTAAA
29184140 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
31 11 0.44
32 6 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATTAATATATAATATAATATTTAAAATT
Found at i:29184130 original size:12 final size:12
Alignment explanation
Indices: 29184113--29184138 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29184103 TTAAAATTAA
29184113 AATATAATATTT
1 AATATAATATTT
29184125 AATATAATATTT
1 AATATAATATTT
29184137 AA
1 AA
29184139 ATTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATAATATTT
Found at i:29193089 original size:18 final size:19
Alignment explanation
Indices: 29193066--29193111 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
29193056 AGTTCATGAA
29193066 TTTAATTAAATTTTA-TAT
1 TTTAATTAAATTTTATTAT
*
29193084 TTTAA-TATATTTTTATTAT
1 TTTAATTA-AATTTTATTAT
*
29193103 CTTAATTAA
1 TTTAATTAA
29193112 TACAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 11 0.48
19 8 0.35
20 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATTAAATTTTATTAT
Found at i:29198462 original size:15 final size:14
Alignment explanation
Indices: 29198389--29198463 Score: 60
Period size: 15 Copynumber: 5.0 Consensus size: 14
29198379 CCTGCTGCTT
29198389 CTGTTGTTTCTGTTG
1 CTGTTGTTT-TGTTG
*
29198404 CTCTTGATTTTGTTG
1 CTGTTG-TTTTGTTG
* *
29198419 CTGCTGATGTTGTTG
1 CTGTTG-TTTTGTTG
* *
29198434 CTGTCGTTGCTGTTG
1 CTGTTGTT-TTGTTG
29198449 CTGTTGCTTTTGTTG
1 CTGTTG-TTTTGTTG
29198464 TGGTTGGAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
14 1 0.02
15 41 0.87
16 5 0.11
ACGTcount: A:0.03, C:0.15, G:0.28, T:0.55
Consensus pattern (14 bp):
CTGTTGTTTTGTTG
Found at i:29198463 original size:21 final size:21
Alignment explanation
Indices: 29198392--29198463 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
29198382 GCTGCTTCTG
* * *
29198392 TTGTTTCTGTTGCTCTTGATT
1 TTGTTGCTGTTGCTGTTGCTT
* *
29198413 TTGTTGCTGCTGATGTTGTTGCTG
1 TTGTTGCTG-T--TGCTGTTGCTT
*
29198437 TCGTTGCTGTTGCTGTTGCTT
1 TTGTTGCTGTTGCTGTTGCTT
29198458 TTGTTG
1 TTGTTG
29198464 TGGTTGGAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
21 22 0.56
22 1 0.03
23 1 0.03
24 15 0.38
ACGTcount: A:0.03, C:0.14, G:0.28, T:0.56
Consensus pattern (21 bp):
TTGTTGCTGTTGCTGTTGCTT
Found at i:29198810 original size:2 final size:2
Alignment explanation
Indices: 29198803--29198872 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
29198793 AAATTAATTG
29198803 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29198845 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29198873 GCATAGCTAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29217586 original size:50 final size:50
Alignment explanation
Indices: 29217523--29217624 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
29217513 ATAAGATAAA
* * *
29217523 ATGATATTATTTAATCTAATTTTATTTATTATATTATTTTAGCATATCTT
1 ATGACATTATTTAATCTAATCTTATTTATAATATTATTTTAGCATATCTT
**
29217573 ATGACATTATTTAATCTAATCTTATTTATAATATTATTTTATTATATCTT
1 ATGACATTATTTAATCTAATCTTATTTATAATATTATTTTAGCATATCTT
29217623 AT
1 AT
29217625 AATAATCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (50 bp):
ATGACATTATTTAATCTAATCTTATTTATAATATTATTTTAGCATATCTT
Found at i:29217608 original size:27 final size:26
Alignment explanation
Indices: 29217526--29217624 Score: 71
Period size: 27 Copynumber: 3.8 Consensus size: 26
29217516 AGATAAAATG
* *
29217526 ATATTATTTAATCTAATTTTATTTATT
1 ATATTATTTAAT-TAATCTTATTTATA
* * *
29217553 ATATTA-TT--TT-AGCATATCTTATG
1 ATATTATTTAATTAATCTTAT-TTATA
*
29217576 ACATTATTTAATCTAATCTTATTTATA
1 ATATTATTTAAT-TAATCTTATTTATA
*
29217603 ATATTATTTTATTATATCTTAT
1 ATATTATTTAATTA-ATCTTAT
29217625 AATAATCTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
22 4 0.07
23 10 0.18
24 3 0.05
26 5 0.09
27 28 0.51
28 5 0.09
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (26 bp):
ATATTATTTAATTAATCTTATTTATA
Found at i:29218481 original size:23 final size:22
Alignment explanation
Indices: 29218451--29218494 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
29218441 AATAATAATT
29218451 TTTTTTA-TAATTATATACTCTTC
1 TTTTTTATTAA-TATAT-CTCTTC
29218474 TTTTTTATTAATATATCTCTT
1 TTTTTTATTAATATATCTCTT
29218495 ATACATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 12 0.60
24 3 0.15
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTTATTAATATATCTCTTC
Found at i:29219080 original size:22 final size:21
Alignment explanation
Indices: 29219055--29219097 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29219045 AAAGATTTTT
29219055 TTTTTAAATTTTTGATTGAATG
1 TTTTT-AATTTTTGATTGAATG
29219077 TTTTTAATTTTTGATTGAATG
1 TTTTTAATTTTTGATTGAATG
29219098 AGATCTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TTTTTAATTTTTGATTGAATG
Found at i:29219966 original size:23 final size:23
Alignment explanation
Indices: 29219936--29219980 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
29219926 TTTACTATAA
*
29219936 GCCCATAAAAAATAATTCTTTTG
1 GCCCATAAAAAATAATGCTTTTG
*
29219959 GCCCATAAATAATAATGCTTTT
1 GCCCATAAAAAATAATGCTTTT
29219981 ATTTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
GCCCATAAAAAATAATGCTTTTG
Found at i:29220180 original size:14 final size:15
Alignment explanation
Indices: 29220152--29220184 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29220142 ATGAATAATT
*
29220152 TTTTAACTATGAATA
1 TTTTAACTATAAATA
29220167 TTTT-ACTATAAATA
1 TTTTAACTATAAATA
29220181 TTTT
1 TTTT
29220185 TTCTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTAACTATAAATA
Found at i:29225361 original size:11 final size:11
Alignment explanation
Indices: 29225345--29225374 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29225335 TTCAAGGAAA
*
29225345 ATTTATATTAT
1 ATTTATATTAG
29225356 ATTTATATTAG
1 ATTTATATTAG
29225367 ATTTATAT
1 ATTTATAT
29225375 ACCATTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (11 bp):
ATTTATATTAG
Found at i:29226778 original size:26 final size:25
Alignment explanation
Indices: 29226749--29226798 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
29226739 TTTAAGTGAA
29226749 ATTC-TTAAAATTGTTTAATAAAAATG
1 ATTCATTAAAA-T-TTTAATAAAAATG
29226775 ATTCAATTAAAATTTTAATAAAAA
1 ATTC-ATTAAAATTTTAATAAAAA
29226799 AATTATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.68
27 1 0.05
28 6 0.27
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTCATTAAAATTTTAATAAAAATG
Found at i:29226851 original size:22 final size:22
Alignment explanation
Indices: 29226826--29226868 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29226816 CGATAGAATT
* *
29226826 TAAAGAAAAAATCAATAATATG
1 TAAAAAAAAAATCAAAAATATG
*
29226848 TAAAAAAAAAATTAAAAATAT
1 TAAAAAAAAAATCAAAAATAT
29226869 CATTTATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (22 bp):
TAAAAAAAAAATCAAAAATATG
Found at i:29227932 original size:22 final size:22
Alignment explanation
Indices: 29227907--29227948 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29227897 GAAAATTTTA
29227907 AATC-TGATTTGAATTTGAATCG
1 AATCTTGATTTG-ATTTGAATCG
*
29227929 AATCTTTATTTGATTTGAAT
1 AATCTTGATTTGATTTGAAT
29227949 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (22 bp):
AATCTTGATTTGATTTGAATCG
Found at i:29227965 original size:21 final size:22
Alignment explanation
Indices: 29227918--29227970 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
29227908 ATCTGATTTG
** *
29227918 AATTTGAATCGAATCTTTATTT
1 AATTTGAATTAAATCTTTATTA
*
29227940 GATTTGAATTAAAT-TTTATTA
1 AATTTGAATTAAATCTTTATTA
*
29227961 AATTTTAATT
1 AATTTGAATT
29227971 TTTTAATATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (22 bp):
AATTTGAATTAAATCTTTATTA
Found at i:29228780 original size:16 final size:17
Alignment explanation
Indices: 29228761--29228793 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29228751 TCATTTTTAA
*
29228761 AAATTAATA-TTTATTT
1 AAATTAAAATTTTATTT
29228777 AAATTAAAATTTTATTT
1 AAATTAAAATTTTATTT
29228794 TTAAGATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTAAAATTTTATTT
Found at i:29234703 original size:2 final size:2
Alignment explanation
Indices: 29234696--29234729 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29234686 TCTGTGATTC
29234696 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
29234730 TGTAATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29235356 original size:63 final size:63
Alignment explanation
Indices: 29235256--29235376 Score: 206
Period size: 63 Copynumber: 1.9 Consensus size: 63
29235246 GGACTTCCTT
* * * *
29235256 TTTACATTACCAAACCATTAGGTGGTTTATGTTTGTCATTTATCTTTTTTATTGCTTGTTAGA
1 TTTACATTACCAAACCATTAGGTGGTGTATGTCTGTCACTTATCTTTGTTATTGCTTGTTAGA
29235319 TTTACATTACCAAACCATTAGGTGGTGTATGTCTGTCACTTATCTTTGTTATTGCTTG
1 TTTACATTACCAAACCATTAGGTGGTGTATGTCTGTCACTTATCTTTGTTATTGCTTG
29235377 CTAGTTGTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48
Consensus pattern (63 bp):
TTTACATTACCAAACCATTAGGTGGTGTATGTCTGTCACTTATCTTTGTTATTGCTTGTTAGA
Found at i:29237838 original size:4 final size:4
Alignment explanation
Indices: 29237829--29237855 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29237819 AGAACAAATA
29237829 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
29237856 ATGTAGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:29247082 original size:12 final size:11
Alignment explanation
Indices: 29247055--29247084 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29247045 TCATGTATTG
29247055 ATTTTTATAAA
1 ATTTTTATAAA
29247066 ATTTTTATAAA
1 ATTTTTATAAA
29247077 ATTTTTAT
1 ATTTTTAT
29247085 TTTAATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTTTATAAA
Found at i:29248967 original size:18 final size:18
Alignment explanation
Indices: 29248941--29248976 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29248931 TTTTAAGTAT
29248941 ATAACTGATTTATAGAAA
1 ATAACTGATTTATAGAAA
*
29248959 ATAATTGATTTATAGAAA
1 ATAACTGATTTATAGAAA
29248977 TTATCTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (18 bp):
ATAACTGATTTATAGAAA
Found at i:29255282 original size:15 final size:15
Alignment explanation
Indices: 29255262--29255293 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29255252 GAAATCGAAG
29255262 CTTCTAAACATATCA
1 CTTCTAAACATATCA
29255277 CTTCTAAACATATCA
1 CTTCTAAACATATCA
29255292 CT
1 CT
29255294 AATAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (15 bp):
CTTCTAAACATATCA
Found at i:29261124 original size:33 final size:34
Alignment explanation
Indices: 29261082--29261151 Score: 106
Period size: 35 Copynumber: 2.1 Consensus size: 34
29261072 TTCCTGTTAG
* *
29261082 TATATATG-TATATTTACTTCATACTATACTAAA
1 TATAGATGATATATTTACTTCATACTATACAAAA
29261115 TATAGATGTATATATTTACTTCATACTATACAAAA
1 TATAGATG-ATATATTTACTTCATACTATACAAAA
29261150 TA
1 TA
29261152 CAAGTACAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 7 0.21
35 26 0.79
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (34 bp):
TATAGATGATATATTTACTTCATACTATACAAAA
Found at i:29261305 original size:84 final size:84
Alignment explanation
Indices: 29261164--29261330 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 84
29261154 AGTACAACTT
*
29261164 CAAATAACTTCATCTCCTACCATCTTTCACATTAATTATGTAACATAATAGATCCTTAATTAATT
1 CAAATAACTTCATCTCCTACCACCTTTCACATTAATTATGTAACATAATAGATCCTTAATTAATT
29261229 TCACAGCCATGGTTTTCAG
66 TCACAGCCATGGTTTTCAG
*
29261248 CAAATAACTTCATCTCCTACCACCTTTCACATTAATTATGTAACATAATGGATCCTTAATTAATT
1 CAAATAACTTCATCTCCTACCACCTTTCACATTAATTATGTAACATAATAGATCCTTAATTAATT
29261313 TCACAGCCATGGTTTTCA
66 TCACAGCCATGGTTTTCA
29261331 TGGCTGGAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (84 bp):
CAAATAACTTCATCTCCTACCACCTTTCACATTAATTATGTAACATAATAGATCCTTAATTAATT
TCACAGCCATGGTTTTCAG
Found at i:29263403 original size:15 final size:15
Alignment explanation
Indices: 29263383--29263412 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29263373 CAAACTCTCA
29263383 CCGTGTGTTAACTTT
1 CCGTGTGTTAACTTT
29263398 CCGTGTGTTAACTTT
1 CCGTGTGTTAACTTT
29263413 ATCATTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (15 bp):
CCGTGTGTTAACTTT
Found at i:29268914 original size:22 final size:22
Alignment explanation
Indices: 29268877--29268922 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
29268867 GCTTAAAGAA
29268877 TTTTAAGATAACTTTTGATATAT
1 TTTTAAGATAACTTTTGATA-AT
*
29268900 TTTTAAGATTA-TTTTGATAAT
1 TTTTAAGATAACTTTTGATAAT
29268921 TT
1 TT
29268923 AACTACTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTTAAGATAACTTTTGATAAT
Found at i:29270867 original size:13 final size:13
Alignment explanation
Indices: 29270840--29270868 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29270830 GAGAAAAGAC
29270840 TTTGTGTAAAATT
1 TTTGTGTAAAATT
29270853 TTTG-GTAAAATT
1 TTTGTGTAAAATT
29270865 TTTG
1 TTTG
29270869 GGTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (13 bp):
TTTGTGTAAAATT
Found at i:29272278 original size:17 final size:18
Alignment explanation
Indices: 29272252--29272287 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
29272242 AAATTTTTTA
29272252 TTTTTATTTTTC-TTTCC
1 TTTTTATTTTTCTTTTCC
29272269 TTTTT-TTTTTCTTTTCC
1 TTTTTATTTTTCTTTTCC
29272286 TT
1 TT
29272288 GCTTATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTATTTTTCTTTTCC
Found at i:29275827 original size:46 final size:46
Alignment explanation
Indices: 29275774--29275867 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
29275764 ATCATAAAAA
29275774 GATTGGACTCGATCTTTCATTGTAAGGTATAGAGAAGAATGTAACG
1 GATTGGACTCGATCTTTCATTGTAAGGTATAGAGAAGAATGTAACG
*
29275820 GATTGGACTCGATCTTTCATTGTAAGGTATGGAGAAGAATGTAACG
1 GATTGGACTCGATCTTTCATTGTAAGGTATAGAGAAGAATGTAACG
29275866 GA
1 GA
29275868 GTCTTTTAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (46 bp):
GATTGGACTCGATCTTTCATTGTAAGGTATAGAGAAGAATGTAACG
Found at i:29280810 original size:41 final size:40
Alignment explanation
Indices: 29280683--29280836 Score: 150
Period size: 41 Copynumber: 3.8 Consensus size: 40
29280673 AAAATATTTT
** * * *
29280683 GCTT-AAAAAAAAATTTTCAAGTTGAAAACTTAAAAGGCAT
1 GCTTGAAAAAAAAAAGTTCAAATTGAAAACCTAAAAGGC-G
* *
29280723 GCTTGAAGAAAAAAAGTTCAAATTGAAAACTTGAAAAGGCG
1 GCTTGAAAAAAAAAAGTTCAAATTGAAAACCT-AAAAGGCG
*
29280764 ACTTGAAAAAAAAAAGTTCAAATTGAAAACCTAAAAGGACG
1 GCTTGAAAAAAAAAAGTTCAAATTGAAAACCTAAAAGG-CG
* * *
29280805 GCTTGAGCTAAAAAAAA-TTCAAGTTAAAAACC
1 GCTTGA--AAAAAAAAAGTTCAAATTGAAAACC
29280837 CGAAAGGGCA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
40 10 0.10
41 59 0.61
42 20 0.21
43 8 0.08
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (40 bp):
GCTTGAAAAAAAAAAGTTCAAATTGAAAACCTAAAAGGCG
Found at i:29280818 original size:42 final size:40
Alignment explanation
Indices: 29280689--29280863 Score: 136
Period size: 41 Copynumber: 4.2 Consensus size: 40
29280679 TTTTGCTTAA
* * * *
29280689 AAAAAAATTTTCAAGTTGAAAACTTAAAAGGCATGCTTGAAG-
1 AAAAAAA-GTTCAAATTGAAAACCTAAAAGGC-GGCTTG-AGC
* * **
29280731 AAAAAAAGTTCAAATTGAAAACTTGAAAAGGCGACTTGAAA
1 AAAAAAAGTTCAAATTGAAAACCT-AAAAGGCGGCTTGAGC
29280772 AAAAAAAGTTCAAATTGAAAACCTAAAAGGACGGCTTGAGC
1 AAAAAAAGTTCAAATTGAAAACCTAAAAGG-CGGCTTGAGC
* * * * * *
29280813 TAAAAAAAATTCAAGTTAAAAACCCGAAAGGGCAGCTTGAGCC
1 -AAAAAAAGTTCAAATTGAAAA-CCTAAAAGGCGGCTTGAG-C
29280856 AAACAAAA
1 AAA-AAAA
29280864 AAGAAAAAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
40 7 0.06
41 49 0.44
42 43 0.39
43 12 0.11
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (40 bp):
AAAAAAAGTTCAAATTGAAAACCTAAAAGGCGGCTTGAGC
Found at i:29280843 original size:82 final size:82
Alignment explanation
Indices: 29280687--29280841 Score: 179
Period size: 82 Copynumber: 1.9 Consensus size: 82
29280677 TATTTTGCTT
** * * * * *
29280687 AAAAAAAAATTTTCAAGTTGAAAACTTAAAAGGCATGCTTGAAGAAAAAAAGTTCAAATTGAAAA
1 AAAAAAAAAAGTTCAAATTGAAAACCTAAAAGGCAGGCTTGAAGAAAAAAAATTCAAATTAAAAA
**
29280752 CTTGAAAAGGCGACTTG
66 CCCGAAAAGGCGACTTG
*
29280769 AAAAAAAAAAGTTCAAATTGAAAACCTAAAAGG-ACGGCTTG-AGCTAAAAAAAATTCAAGTTAA
1 AAAAAAAAAAGTTCAAATTGAAAACCTAAAAGGCA-GGCTTGAAG--AAAAAAAATTCAAATTAA
29280832 AAACCCGAAA
63 AAACCCGAAA
29280842 GGGCAGCTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
81 3 0.05
82 34 0.57
83 23 0.38
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (82 bp):
AAAAAAAAAAGTTCAAATTGAAAACCTAAAAGGCAGGCTTGAAGAAAAAAAATTCAAATTAAAAA
CCCGAAAAGGCGACTTG
Found at i:29281972 original size:56 final size:57
Alignment explanation
Indices: 29281912--29282030 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 57
29281902 GCCCAGATTA
* * * * *
29281912 TTTTTTCAAACTTATGATTTAATTTTGATCGTTTGATCT-TGGCTCGTTCTAGATC-T
1 TTTTTTCAAACTTACGATTCAATCTCGATCGTTTGAT-TATGGCTCGATCTAGATCAT
* *
29281968 TTTTTTCAAACTTACGATTCAATCTCGATTGTTTGATTATGGCTTGATCTAGATCAT
1 TTTTTTCAAACTTACGATTCAATCTCGATCGTTTGATTATGGCTCGATCTAGATCAT
29282025 TTTTTT
1 TTTTTT
29282031 AGATTTTACT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 1 0.02
56 46 0.85
57 7 0.13
ACGTcount: A:0.21, C:0.14, G:0.13, T:0.51
Consensus pattern (57 bp):
TTTTTTCAAACTTACGATTCAATCTCGATCGTTTGATTATGGCTCGATCTAGATCAT
Found at i:29283121 original size:23 final size:22
Alignment explanation
Indices: 29283079--29283133 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
29283069 TTTCCTTTTT
*
29283079 TCATTTTATTTTTATTTTTTAA
1 TCATTTTATTTTTATGTTTTAA
29283101 TCATTTTATATTTTATGTTTT--
1 TCATTTTAT-TTTTATGTTTTAA
*
29283122 TTATTTTATTTT
1 TCATTTTATTTT
29283134 CAATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 8 0.27
22 9 0.30
23 10 0.33
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (22 bp):
TCATTTTATTTTTATGTTTTAA
Found at i:29283121 original size:24 final size:22
Alignment explanation
Indices: 29283079--29283142 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
29283069 TTTCCTTTTT
29283079 TCATTTTATTTTTATTTTTTAA
1 TCATTTTATTTTTATTTTTTAA
29283101 TCATTTTATATTTTATGTTTTT--
1 TCATTTTAT-TTTTAT-TTTTTAA
*
29283123 T-ATTTTATTTTCAATTTTTT
1 TCATTTTATTTT-TATTTTTT
29283143 TATTTATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 8 0.21
21 9 0.24
22 10 0.26
23 6 0.16
24 5 0.13
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (22 bp):
TCATTTTATTTTTATTTTTTAA
Found at i:29287296 original size:50 final size:49
Alignment explanation
Indices: 29287212--29287316 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 49
29287202 AAGTTTAAAC
* * *
29287212 ACACATGTTAAGTCAAAAATAACTGTCAAACATAAGACAATATAAAAAG
1 ACACTTGTTAAGTCAAAAACAACTGTCAAACATAAAACAATATAAAAAG
* * *
29287261 ACACTTGTTGAAGTCAAAGACAATTGTCAAACATAAAATAATATAAAAAG
1 ACACTTGTT-AAGTCAAAAACAACTGTCAAACATAAAACAATATAAAAAG
29287311 ACACTT
1 ACACTT
29287317 ATAAGAAGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 8 0.16
50 41 0.84
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.23
Consensus pattern (49 bp):
ACACTTGTTAAGTCAAAAACAACTGTCAAACATAAAACAATATAAAAAG
Found at i:29296718 original size:38 final size:38
Alignment explanation
Indices: 29296667--29296744 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
29296657 GGAGGGAAAG
*
29296667 ATTAAATATGTATCACAAGCAAATCTACATCAAAGCTT
1 ATTAAATATGTATCACAAGCAAATCTACATCAAAACTT
*
29296705 ATTAAATATGTATCGCAAGCAAATCTACATCAAAACTT
1 ATTAAATATGTATCACAAGCAAATCTACATCAAAACTT
29296743 AT
1 AT
29296745 CAAAAGAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (38 bp):
ATTAAATATGTATCACAAGCAAATCTACATCAAAACTT
Found at i:29298451 original size:27 final size:27
Alignment explanation
Indices: 29298395--29298451 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
29298385 ATTATACTTT
**
29298395 TAAAAATTATATAAATAATTTAAATTA
1 TAAAAATTATATAAATAATTTAAAAAA
* *
29298422 TAAAATTTATATAAAT-TTTTAAGAAAA
1 TAAAAATTATATAAATAATTTAA-AAAA
29298449 TAA
1 TAA
29298452 TTTTGATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAAAATTATATAAATAATTTAAAAAA
Found at i:29298946 original size:39 final size:38
Alignment explanation
Indices: 29298903--29298993 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 38
29298893 AAATACTAAA
29298903 AATATAACAAAACCTAAACTA-AAAAAGTAAAAACAATAT
1 AATATAACAAAACCTAAACTATAAAAAGTAAAAA-AA-AT
* * *
29298942 AATATAATAAAACCTAAACTATAAAAGGTGAAAAAAAT
1 AATATAACAAAACCTAAACTATAAAAAGTAAAAAAAAT
*
29298980 AATAAAACCAAAAC
1 AATATAA-CAAAAC
29298994 TAATAAATTG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 8 0.18
39 27 0.60
40 10 0.22
ACGTcount: A:0.66, C:0.12, G:0.04, T:0.18
Consensus pattern (38 bp):
AATATAACAAAACCTAAACTATAAAAAGTAAAAAAAAT
Found at i:29299455 original size:21 final size:22
Alignment explanation
Indices: 29299429--29299471 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29299419 ATTCGAATTT
*
29299429 TAAACCTC-ATTTTAAAAAAAA
1 TAAACCTCTATTTAAAAAAAAA
29299450 TAAACCTCTATTTAAAAAAAAA
1 TAAACCTCTATTTAAAAAAAAA
29299472 AAGAAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAACCTCTATTTAAAAAAAAA
Found at i:29302949 original size:21 final size:21
Alignment explanation
Indices: 29302911--29302950 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29302901 TGAAGTACAC
29302911 AATGATATAAACAAAAAAAGT
1 AATGATATAAACAAAAAAAGT
*
29302932 AATGA-ATGAACAACAAAAA
1 AATGATATAAACAA-AAAAA
29302951 TAGTTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (21 bp):
AATGATATAAACAAAAAAAGT
Found at i:29303449 original size:20 final size:20
Alignment explanation
Indices: 29303383--29303455 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
29303373 TTAAGCAATC
* *
29303383 GATCGATCCCTTTAAGAGGGG
1 GATCGATCCC-TTACGTGGGG
* * * *
29303404 G-TCAATCCCTTACCATAGGT
1 GATCGATCCCTTA-CGTGGGG
29303424 GATCGATCCCTTACGTGGGG
1 GATCGATCCCTTACGTGGGG
29303444 GATCGATCCCTT
1 GATCGATCCCTT
29303456 TTCTGAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.08
20 26 0.65
21 11 0.28
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (20 bp):
GATCGATCCCTTACGTGGGG
Found at i:29307061 original size:13 final size:13
Alignment explanation
Indices: 29307043--29307067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29307033 TTTTGATTTT
29307043 AATCGAATTAATC
1 AATCGAATTAATC
29307056 AATCGAATTAAT
1 AATCGAATTAAT
29307068 TTAATTCAAT
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:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
AATCGAATTAATC
Found at i:29307144 original size:13 final size:14
Alignment explanation
Indices: 29307118--29307146 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29307108 CAGTTAATCA
29307118 AAAATTATTTTTTT
1 AAAATTATTTTTTT
29307132 AAAATTATTTTTTT
1 AAAATTATTTTTTT
29307146 A
1 A
29307147 TTTTTTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AAAATTATTTTTTT
Found at i:29307336 original size:26 final size:26
Alignment explanation
Indices: 29307283--29307336 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
29307273 AATAAATTCT
**
29307283 AAAATTTTCAAAATGTTGATTTTTAA
1 AAAATTTTCAAAATGTTGATTTAAAA
*
29307309 AAAATTTTTAAAATG-TGATTTAAAA
1 AAAATTTTCAAAATGTTGATTTAAAA
29307334 AAA
1 AAA
29307337 GTATGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (26 bp):
AAAATTTTCAAAATGTTGATTTAAAA
Found at i:29308193 original size:21 final size:21
Alignment explanation
Indices: 29308152--29308193 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29308142 ATGTCAATAT
**
29308152 TTATAATTTTTTATTTTAAAA
1 TTATAATTTTTTATTAAAAAA
*
29308173 TTATGATTTTTTATTAAAAAA
1 TTATAATTTTTTATTAAAAAA
29308194 ATTGTCTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTATAATTTTTTATTAAAAAA
Found at i:29316875 original size:16 final size:16
Alignment explanation
Indices: 29316851--29316917 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 16
29316841 TTTTAATTAA
*
29316851 TTATTTAATTATATAT
1 TTATATAATTATATAT
* *
29316867 TTATATAATGATATTT
1 TTATATAATTATATAT
*
29316883 TTAAAT-ATT-TATAT
1 TTATATAATTATATAT
* * *
29316897 TTAAAAAATAATAT-T
1 TTATATAATTATATAT
29316912 TTATAT
1 TTATAT
29316918 TAAAAAATAA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
14 9 0.23
15 9 0.23
16 21 0.54
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
TTATATAATTATATAT
Found at i:29316916 original size:21 final size:20
Alignment explanation
Indices: 29316886--29316935 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
29316876 GATATTTTTA
29316886 AATA-TTTATATTTAAAAAAT
1 AATATTTTATA-TTAAAAAAT
29316906 AATATTTTATATTAAAAAAT
1 AATATTTTATATTAAAAAAT
29316926 AATATTTTAT
1 AATATTTTAT
29316936 TAATTTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTTATATTAAAAAAT
Found at i:29326172 original size:57 final size:57
Alignment explanation
Indices: 29326084--29326256 Score: 319
Period size: 57 Copynumber: 3.0 Consensus size: 57
29326074 TGTAATGCCC
29326084 AATTCAGATTAAGATGAAGCTTGTATAACTTTAAGAAAAAGTATAAACAAAAGAACT
1 AATTCAGATTAAGATGAAGCTTGTATAACTTTAAGAAAAAGTATAAACAAAAGAACT
*
29326141 AATTCAGATTAAGATGAAGCTTGTATAACTTTAAGAAAAAGCATAAACAAAAGAACT
1 AATTCAGATTAAGATGAAGCTTGTATAACTTTAAGAAAAAGTATAAACAAAAGAACT
* *
29326198 AATTCAGATTAAGATGAAGCTTGTATAACTTTAAGAAAAAGTTTAAACACAAGAACT
1 AATTCAGATTAAGATGAAGCTTGTATAACTTTAAGAAAAAGTATAAACAAAAGAACT
29326255 AA
1 AA
29326257 CATAACACAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 112 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (57 bp):
AATTCAGATTAAGATGAAGCTTGTATAACTTTAAGAAAAAGTATAAACAAAAGAACT
Found at i:29327716 original size:3 final size:3
Alignment explanation
Indices: 29327703--29327733 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
29327693 CTTTCCGCTA
*
29327703 CCG CTG CCG CCG CCG CCG CCG CCG CCG CCG C
1 CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG C
29327734 TGCTCCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.65, G:0.32, T:0.03
Consensus pattern (3 bp):
CCG
Found at i:29335530 original size:29 final size:26
Alignment explanation
Indices: 29335498--29335561 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 26
29335488 TATGTTAAAT
29335498 TTAAATTATATTAAATATTAAGAATATTA
1 TTAAATTA-ATTAAAT-TTAAGAATA-TA
*
29335527 TTAATAATTAATTAAATTTATGAATATA
1 TT-A-AATTAATTAAATTTAAGAATATA
*
29335555 ATAAATT
1 TTAAATT
29335562 TATGAATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
28 3 0.10
29 10 0.32
30 8 0.26
31 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
TTAAATTAATTAAATTTAAGAATATA
Found at i:29335577 original size:16 final size:15
Alignment explanation
Indices: 29335537--29335585 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 15
29335527 TTAATAATTA
29335537 ATTAAATTTATGAAT
1 ATTAAATTTATGAAT
29335552 ATAATAAATTTATGAAT
1 AT--TAAATTTATGAAT
*
29335569 GATTAAATTCATGAAT
1 -ATTAAATTTATGAAT
29335585 A
1 A
29335586 ATTTGATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 3 0.10
16 12 0.40
17 13 0.43
18 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (15 bp):
ATTAAATTTATGAAT
Found at i:29337882 original size:27 final size:28
Alignment explanation
Indices: 29337851--29337907 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
29337841 TATGATAAAA
29337851 AATAATATTT-TAA-TTATTATATTA-ATT
1 AATAA-ATTTATAATTTA-TATATTATATT
29337878 AATAAATTTATAATTTATATATTATATT
1 AATAAATTTATAATTTATATATTATATT
29337906 AA
1 AA
29337908 ACATTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.15
27 15 0.56
28 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AATAAATTTATAATTTATATATTATATT
Found at i:29338334 original size:27 final size:26
Alignment explanation
Indices: 29338300--29338354 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
29338290 AAATATTTTA
*
29338300 ATTAATATAA-TATTTTAAAATTATTT
1 ATTAATATAATTA-TTTAAAATTAATT
*
29338326 ATTATATATTATTATTTAAAATTAATT
1 ATTA-ATATAATTATTTAAAATTAATT
29338353 AT
1 AT
29338355 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 19 0.76
28 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTAATATAATTATTTAAAATTAATT
Found at i:29345064 original size:2 final size:2
Alignment explanation
Indices: 29345057--29345112 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
29345047 CAGATGGAGA
* * * *
29345057 AT AT AT AT AA AT AA AT AA AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29345099 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
29345113 CCTCTAAATC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:29346443 original size:15 final size:15
Alignment explanation
Indices: 29346423--29346454 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29346413 GTATTGGTTT
29346423 TATTACAATTATTTG
1 TATTACAATTATTTG
29346438 TATTACAATTATTTG
1 TATTACAATTATTTG
29346453 TA
1 TA
29346455 AATTCAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (15 bp):
TATTACAATTATTTG
Found at i:29347999 original size:19 final size:19
Alignment explanation
Indices: 29347959--29348000 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
29347949 GATCCTGAAG
*
29347959 TATTTTATTTATTATTTGT
1 TATTTTATTTATTATGTGT
*
29347978 TATTTTCTTTATTTATGT-T
1 TATTTTATTTA-TTATGTGT
29347997 TATT
1 TATT
29348001 GTTTAGTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (19 bp):
TATTTTATTTATTATGTGT
Found at i:29358038 original size:51 final size:52
Alignment explanation
Indices: 29357944--29358047 Score: 149
Period size: 51 Copynumber: 2.0 Consensus size: 52
29357934 TATAAGCATA
*
29357944 CAAACTTGCCTATTAAAAATATTTTTTCTCTTAGAATTTTTCTTTTGTAAGT
1 CAAACTTGCCTATTAAAAATATTTTTTCTCTTAGAATTATTCTTTTGTAAGT
* * *
29357996 CAAATTTGCCTATTAGAAATCTCTTTTT-T-TTAGAATTATTCTTTTGTAAGT
1 CAAACTTGCCTATTAAAAATAT-TTTTTCTCTTAGAATTATTCTTTTGTAAGT
29358047 C
1 C
29358048 TTTTTGTCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
51 22 0.47
52 20 0.43
53 5 0.11
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (52 bp):
CAAACTTGCCTATTAAAAATATTTTTTCTCTTAGAATTATTCTTTTGTAAGT
Found at i:29359187 original size:13 final size:14
Alignment explanation
Indices: 29359169--29359203 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
29359159 GAGGACTCAT
29359169 CTTTATGATATA-A
1 CTTTATGATATAGA
29359182 CTTTATGATATAGA
1 CTTTATGATATAGA
29359196 C-TTATGAT
1 CTTTATGAT
29359204 CGAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.90
14 2 0.10
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (14 bp):
CTTTATGATATAGA
Found at i:29364069 original size:20 final size:21
Alignment explanation
Indices: 29364044--29364085 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
29364034 TTAATATAAA
29364044 AATT-AATTTTATTTATC-AAT
1 AATTAAATTTT-TTTATCTAAT
29364064 AATTAAATTTTTTTATCTAAT
1 AATTAAATTTTTTTATCTAAT
29364085 A
1 A
29364086 TGAGATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTAAATTTTTTTATCTAAT
Found at i:29370309 original size:30 final size:30
Alignment explanation
Indices: 29370259--29370316 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29370249 AAGAGTAAAG
*
29370259 TAAATTAATAGTTATCCTTATATTGACCAA
1 TAAATTAATACTTATCCTTATATTGACCAA
* *
29370289 TAAATTGATACTTATTCTTATATTGACC
1 TAAATTAATACTTATCCTTATATTGACC
29370317 CACTTTGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (30 bp):
TAAATTAATACTTATCCTTATATTGACCAA
Found at i:29375747 original size:18 final size:18
Alignment explanation
Indices: 29375726--29375760 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29375716 ATTTAATATT
29375726 TTTAAAAAAATTAAATTG
1 TTTAAAAAAATTAAATTG
**
29375744 TTTAAAATTATTAAATT
1 TTTAAAAAAATTAAATT
29375761 ATTAATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTAAAAAAATTAAATTG
Found at i:29375906 original size:9 final size:9
Alignment explanation
Indices: 29375892--29375922 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29375882 AGATATTTAA
29375892 TTTGAAAAT
1 TTTGAAAAT
29375901 TTTGAAAAT
1 TTTGAAAAT
*
29375910 TTTAAAAAT
1 TTTGAAAAT
29375919 TTTG
1 TTTG
29375923 CATTTATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (9 bp):
TTTGAAAAT
Found at i:29377080 original size:31 final size:31
Alignment explanation
Indices: 29377020--29377080 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
29377010 TTTAATTATA
* *
29377020 TATTTTATTTAAATCGAATTCAAACTTTAAT
1 TATTTTATTTAAATCCAATTCAAAATTTAAT
*
29377051 TATTTT-TTTAAGATCCAATTTAAAATTTAA
1 TATTTTATTTAA-ATCCAATTCAAAATTTAA
29377081 ATGCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (31 bp):
TATTTTATTTAAATCCAATTCAAAATTTAAT
Found at i:29378680 original size:12 final size:13
Alignment explanation
Indices: 29378665--29378724 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
29378655 AATATTATTT
29378665 TAAATA-TAAATA
1 TAAATATTAAATA
29378677 TAAA-ATTAAATA
1 TAAATATTAAATA
* *
29378689 TATATA-AAAATA
1 TAAATATTAAATA
*
29378701 TATAAAATTAAATA
1 TA-AATATTAAATA
29378715 TAAA-ATTAAA
1 TAAATATTAAA
29378725 AAAATAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 1 0.03
12 26 0.67
13 5 0.13
14 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:29392873 original size:22 final size:22
Alignment explanation
Indices: 29392829--29392873 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29392819 TAAAATTTTG
* * * *
29392829 ATAAAAATATAATATAATTTAA
1 ATAAAAAAATAAAAAAATATAA
29392851 ATAAAAAAATAAAAAAATATAA
1 ATAAAAAAATAAAAAAATATAA
29392873 A
1 A
29392874 ATTATTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAAAAAAATAAAAAAATATAA
Found at i:29395618 original size:41 final size:42
Alignment explanation
Indices: 29395553--29395637 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
29395543 CATGAATGTG
* * *
29395553 GCTGAAATAGTATTAGCTCTTTGTTTAAATACTAATTTGTAGA
1 GCTGAAATAG-ATTAACTCTTTGTTTAAACACTAATCTGTAGA
*
29395596 GCTGAAATA-ATTAACTCTTTGTTTTAACACTAATCTGTAGA
1 GCTGAAATAGATTAACTCTTTGTTTAAACACTAATCTGTAGA
29395637 G
1 G
29395638 AAAGTGTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 29 0.76
43 9 0.24
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (42 bp):
GCTGAAATAGATTAACTCTTTGTTTAAACACTAATCTGTAGA
Done.