Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 23 of 26
Found at i:3633551 original size:13 final size:13
Alignment explanation
Indices: 3633533--3633576 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
3633523 TAATGATTAG
3633533 ATTTATATATTTT
1 ATTTATATATTTT
*
3633546 ATTTATGTTATTTT
1 ATTTAT-ATATTTT
3633560 ATATT-TATATTTT
1 AT-TTATATATTTT
3633573 ATTT
1 ATTT
3633577 TAAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.07
13 14 0.52
14 9 0.33
15 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
ATTTATATATTTT
Found at i:3633574 original size:18 final size:19
Alignment explanation
Indices: 3633553--3633589 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3633543 TTTATTTATG
*
3633553 TTATTTTATAT-TTATATT
1 TTATTTTAAATATTATATT
3633571 TTATTTTAAATATTATATT
1 TTATTTTAAATATTATATT
3633590 CAAGTCGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTTAAATATTATATT
Found at i:3633829 original size:7 final size:7
Alignment explanation
Indices: 3633817--3633845 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3633807 AGAAGAAGCG
3633817 ATTGAAA
1 ATTGAAA
3633824 ATTGAAA
1 ATTGAAA
3633831 ATTGAAA
1 ATTGAAA
3633838 ATTGAAA
1 ATTGAAA
3633845 A
1 A
3633846 ATAGAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (7 bp):
ATTGAAA
Found at i:3637014 original size:22 final size:24
Alignment explanation
Indices: 3636977--3637028 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
3636967 TTAAAATTTA
*
3636977 TTTTATATTAATAATTAT-ATAAT
1 TTTTATACTAATAATTATAATAAT
* *
3637000 TTTTATACTAA-AATTTTAATTAT
1 TTTTATACTAATAATTATAATAAT
3637023 TTTTAT
1 TTTTAT
3637029 TAATTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATACTAATAATTATAATAAT
Found at i:3639379 original size:73 final size:72
Alignment explanation
Indices: 3639286--3639420 Score: 234
Period size: 73 Copynumber: 1.9 Consensus size: 72
3639276 CAATTTTTTT
* *
3639286 TTCTAATCTTTTTAATTTTCTATGTATAATATGAATTGCTGAATGTCAATTGTTCAATCTTTATC
1 TTCTAATCTTTTTAATTTTCTATATATAATATGAATTGCTGAATGCCAATTGTTCAATCTTTATC
3639351 ATTATAG
66 ATTATAG
*
3639358 TTCTAATCTTTTTTAATTTTCTATATATAATATGTATTGCTGAATGCCAATTGTTCAATCTTT
1 TTCTAATC-TTTTTAATTTTCTATATATAATATGAATTGCTGAATGCCAATTGTTCAATCTTT
3639421 CATTGAGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
72 8 0.14
73 51 0.86
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (72 bp):
TTCTAATCTTTTTAATTTTCTATATATAATATGAATTGCTGAATGCCAATTGTTCAATCTTTATC
ATTATAG
Found at i:3641810 original size:7 final size:7
Alignment explanation
Indices: 3641798--3641831 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
3641788 GGGTTTCGAA
3641798 TAAATTT
1 TAAATTT
3641805 TAAATTT
1 TAAATTT
3641812 TAAATTT
1 TAAATTT
3641819 TAAATTT
1 TAAATTT
3641826 TAAATT
1 TAAATT
3641832 CATGTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TAAATTT
Found at i:3643431 original size:3 final size:3
Alignment explanation
Indices: 3643423--3643452 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3643413 ATTTGGCTCG
3643423 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3643453 TGTTATATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3651454 original size:1 final size:1
Alignment explanation
Indices: 3651448--3651538 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
3651438 AAATCTTCAC
* * ** * * * **
3651448 TTTTTTTTTTTGTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
3651513 TTTTTGTTTTGTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
3651539 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:3651502 original size:33 final size:31
Alignment explanation
Indices: 3651448--3651540 Score: 161
Period size: 33 Copynumber: 3.0 Consensus size: 31
3651438 AAATCTTCAC
3651448 TTTTTTT-TTTTGTTTTTTTTTCTTTTTCCT
1 TTTTTTTGTTTTGTTTTTTTTTCTTTTTCCT
3651478 TTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCT
1 TTTTTTTGTTTTG--TTTTTTTTTCTTTTTCCT
3651511 TTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
1 TTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
3651541 AATTGCCATG
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
30 7 0.12
31 22 0.37
33 31 0.52
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (31 bp):
TTTTTTTGTTTTGTTTTTTTTTCTTTTTCCT
Found at i:3663725 original size:52 final size:52
Alignment explanation
Indices: 3663645--3663764 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
3663635 AAAAGTTGTT
*
3663645 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
3663697 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
3663749 TGCATGTATCGATACA
1 TGCATGTATCGATACA
3663765 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:3663777 original size:52 final size:51
Alignment explanation
Indices: 3663645--3663784 Score: 210
Period size: 52 Copynumber: 2.7 Consensus size: 51
3663635 AAAAGTTGTT
3663645 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
* *
3663697 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
*
3663749 TGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3663785 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:3663791 original size:13 final size:13
Alignment explanation
Indices: 3663773--3663797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3663763 CAAAGATCAG
3663773 TGTATCGATACAA
1 TGTATCGATACAA
3663786 TGTATCGATACA
1 TGTATCGATACA
3663798 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3663879 original size:13 final size:13
Alignment explanation
Indices: 3663861--3663885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3663851 AAAAAAAATA
3663861 TGTATCGATACAT
1 TGTATCGATACAT
3663874 TGTATCGATACA
1 TGTATCGATACA
3663886 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3663984 original size:21 final size:21
Alignment explanation
Indices: 3663943--3663984 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3663933 GTTGGGACCT
*
3663943 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
3663964 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
3663985 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:3666105 original size:52 final size:52
Alignment explanation
Indices: 3666026--3666184 Score: 192
Period size: 52 Copynumber: 3.2 Consensus size: 52
3666016 AAAGCTGAGA
* * *
3666026 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTTAAAGATGG
* *
3666079 AAAAGGTGCCAATATGCTGATTCAAGGCCGGCTATATTGGAC-T-----T--
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTTAAAGATGG
*
3666123 -AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTTAAAGATGG
3666174 AAAAGGTGCCA
1 AAAAGGTGCCA
3666185 CCGATTTGTG
Statistics
Matches: 89, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
43 38 0.43
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 41 0.46
53 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTTAAAGATGG
Found at i:3666141 original size:43 final size:43
Alignment explanation
Indices: 3666080--3666169 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
3666070 TAAAGATGGA
*
3666080 AAAGGTGCCAATATGCTGATTCAAGGCCGGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCGGCTACATTGGACTT
* *
3666123 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCGGCTACATTGGACTT
3666166 AAAG
1 AAAG
3666170 ATGGAAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCGGCTACATTGGACTT
Found at i:3666371 original size:88 final size:87
Alignment explanation
Indices: 3666175--3666432 Score: 380
Period size: 88 Copynumber: 3.0 Consensus size: 87
3666165 TAAAGATGGA
* * * ** *
3666175 AAAGG-TGCCACCGATTTGTGGGC-TTCGAAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAA-TATGCCACTGACTTGTGGGCTTTTGAAAGG
* *
3666236 TTGCCACTGACTTGTGGGCTTTTT
65 GTGCCACTAACTTGTGGGC-TTTT
3666260 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGG
3666325 GTGCCACTAACTTGTGGGCTTTT
65 GTGCCACTAACTTGTGGGCTTTT
3666348 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGG
3666413 GTGCCACTAACTTGTGGGCT
65 GTGCCACTAACTTGTGGGCT
3666433 GAAAAGAGTG
Statistics
Matches: 159, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
85 5 0.03
86 33 0.21
87 12 0.08
88 87 0.55
89 22 0.14
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (87 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGG
TGCCACTAACTTGTGGGCTTTT
Found at i:3666375 original size:58 final size:59
Alignment explanation
Indices: 3666175--3666646 Score: 346
Period size: 58 Copynumber: 8.0 Consensus size: 59
3666165 TAAAGATGGA
* * * *
3666175 AAAGG-TGCCACCGATTTGTGGGC-TTCGAAAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAGGGTGCCACTGACTTGTGGGCTTTTG
* *
3666232 -AAGGTTGCCACTGACTTGTGGGCTTTT-TAAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
** * *
3666289 AAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
***
3666348 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * * * * * **
3666407 AAAAGGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTT----TTG
* * * * * * **
3666468 AAAAAGAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGG
1 --AAAG-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * * *
3666528 AAAAGGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTCG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*** *** *
3666585 AAAAAAAATGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTG
1 --AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
3666645 AA
1 AA
3666647 GGGTGATGAA
Statistics
Matches: 332, Mismatches: 59, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
56 29 0.09
57 62 0.19
58 83 0.25
59 46 0.14
60 71 0.21
61 1 0.00
62 19 0.06
63 1 0.00
64 15 0.05
65 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (59 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
Found at i:3666568 original size:27 final size:27
Alignment explanation
Indices: 3666505--3666651 Score: 105
Period size: 29 Copynumber: 5.1 Consensus size: 27
3666495 TTGGAAAAGA
* *
3666505 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGG
* *
3666535 TGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGG
***
3666562 TGCCACTGACTTGTGGGCTTTCGAAAAAAAA
1 TGCCACTGACTTGTGGGCTTT-G---AAGGG
***
3666593 TGCCACTGACTTGTGGGCTTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTG--AAGGG
*
3666622 TGCCACTGACTTGTGGACTTTTGAAGGG
1 TGCCACTGACTTGTGGGC-TTTGAAGGG
3666650 TG
1 TG
3666652 ATGAATGTCT
Statistics
Matches: 100, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
27 24 0.24
28 5 0.05
29 25 0.25
30 23 0.23
31 23 0.23
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGG
Found at i:3666576 original size:121 final size:117
Alignment explanation
Indices: 3666354--3666637 Score: 320
Period size: 121 Copynumber: 2.4 Consensus size: 117
3666344 TTTTAAAGGT
* **
3666354 TGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCA
1 TGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCA
* *
3666419 CTAACTTGTGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGA
65 CTAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTAC-AAA-AAAAA-A
* * * * * *
3666475 GTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCA
1 -TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCA
* * *** * * *
3666540 CTGATTTGTGGGCTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTCGAAAAAAAA
65 CTAACTTGTGGGCTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACAAAAAAAAA
3666593 TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
1 TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
3666638 ACTTTTGAAG
Statistics
Matches: 136, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
117 39 0.29
118 1 0.01
119 5 0.04
120 3 0.02
121 72 0.53
122 16 0.12
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (117 bp):
TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCAC
TAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACAAAAAAAAA
Found at i:3666645 original size:30 final size:30
Alignment explanation
Indices: 3666173--3666646 Score: 381
Period size: 30 Copynumber: 16.1 Consensus size: 30
3666163 CTTAAAGATG
* * *
3666173 GAAAAGG-TGCCACCGATTTGTGGGC-TTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
3666201 GAAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
*
3666231 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
3666259 -TAAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
3666288 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * *
3666318 GAACAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
*
3666348 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
3666376 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
3666406 GAAAAGGGTGCCACTAACTTGTGGGC---T
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * * **
3666433 GAAAA-GAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GAAAAGGA-TGCCACT-GACTTGTGGGCTT----TT
* * * * *
3666467 GAAAAAGAGTGCCACGGAGTTGTGGACTTTG
1 GAAAAGGA-TGCCACTGACTTGTGGGCTTTT
* **
3666498 GAAAA-GATGCCACCGACTTGTGGGCTTCG
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
3666527 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
3666556 G--AAGGTTGCCACTGACTTGTGGGCTTTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
3666584 GAAAAAAAATGCCACTGACTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
** *
3666614 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
3666644 GAA
1 GAA
3666647 GGGTGATGAA
Statistics
Matches: 369, Mismatches: 52, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.01
27 60 0.16
28 32 0.09
29 82 0.22
30 145 0.39
31 25 0.07
34 5 0.01
35 18 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGATGCCACTGACTTGTGGGCTTTT
Found at i:3668088 original size:1 final size:1
Alignment explanation
Indices: 3668084--3668247 Score: 103
Period size: 1 Copynumber: 164.0 Consensus size: 1
3668074 CCGGACCCCC
* * * * * * * **
3668084 TTTTTTTGTTTGTTTTTTTATTGTTTTTTGTTTTTTGTTTTTTTTTTTTTGTTTTTTTTTTGCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * ** * ** * *
3668149 TTTTTTTGTTTTGTTTTTGTTTTTTTTTTTTTTTTGGTTTTTCTTTTTTTCATTTTTTTTTTCTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** ** *
3668214 GTTTTTCATTTTTTTCGTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3668248 GGAGGACGCC
Statistics
Matches: 121, Mismatches: 42, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 121 1.00
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.85
Consensus pattern (1 bp):
T
Found at i:3668101 original size:11 final size:10
Alignment explanation
Indices: 3668084--3668247 Score: 117
Period size: 11 Copynumber: 16.2 Consensus size: 10
3668074 CCGGACCCCC
3668084 TTTTTTTGTT
1 TTTTTTTGTT
3668094 TGTTTTTT-TAT
1 T-TTTTTTGT-T
3668105 TGTTTTTTGTT
1 T-TTTTTTGTT
*
3668116 TTTTGTTTTTT
1 TTTT-TTTGTT
3668127 TTTTTTTGTTT
1 TTTTTTTG-TT
3668138 TTTTTTTGCTT
1 TTTTTTTG-TT
3668149 TTTTTTTGTT
1 TTTTTTTGTT
3668159 TTGTTTTTG-T
1 TT-TTTTTGTT
3668169 TTTTTTT-TT
1 TTTTTTTGTT
*
3668178 TTTTTTGGTT
1 TTTTTTTGTT
3668188 TTTCTTTT-TT
1 TTT-TTTTGTT
**
3668198 TCATTTT-TT
1 TTTTTTTGTT
* *
3668207 TTTTCTGGTT
1 TTTTTTTGTT
*
3668217 TTTCATTT-TT
1 TTT-TTTTGTT
**
3668227 TTCGTTT-TT
1 TTTTTTTGTT
3668236 TTTTTTTGTT
1 TTTTTTTGTT
3668246 TT
1 TT
3668248 GGAGGACGCC
Statistics
Matches: 124, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
9 31 0.25
10 36 0.29
11 56 0.45
12 1 0.01
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:3668188 original size:29 final size:27
Alignment explanation
Indices: 3668084--3668248 Score: 140
Period size: 28 Copynumber: 5.9 Consensus size: 27
3668074 CCGGACCCCC
* * *
3668084 TTTTTTTGTTTGTTTTTT-TATTGTTT
1 TTTTTTTTTTTTTTTTTTGTTTTGTTT
3668110 TTTGTTTTTTGTTTTTTTTT-TTTTGTTT
1 TTT-TTTTTT-TTTTTTTTTGTTTTGTTT
**
3668138 TTTTTTTGCTTTTTTTTTGTTTTGTTT
1 TTTTTTTTTTTTTTTTTTGTTTTGTTT
3668165 TTGTTTTTTTTTTTTTTTTGGTTTT-TCTT
1 TT-TTTTTTTTTTTTTTTT-GTTTTGT-TT
* *
3668194 TTTTTCATTTTTTTTTTCTGGTTTT-TCATT
1 TTTTT--TTTTTTTTTTTTTGTTTTGT--TT
*
3668224 TTTTTCGTTTTTTTTTTTTGTTTTG
1 TTTTT-TTTTTTTTTTTTTGTTTTG
3668249 GAGGACGCCG
Statistics
Matches: 115, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
26 12 0.10
27 19 0.17
28 36 0.31
29 30 0.26
30 18 0.16
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTTTTGTTTTGTTT
Found at i:3668189 original size:65 final size:63
Alignment explanation
Indices: 3668084--3668249 Score: 178
Period size: 66 Copynumber: 2.6 Consensus size: 63
3668074 CCGGACCCCC
**
3668084 TTTTTTTGTTTGTTTTT-TTATTGTTTTTTGTTTTTT-GTTTTT-TTTTTTTTGTTTTTTTTTTG
1 TTTTTTTGTTTGTTTTTGTT-TT-TTTTTT-TTTTTTGGTTTTTCTTTTTTTCATTTTTTTTTT-
3668146 CTT
62 C-T
3668149 TTTTTTTGTTTTGTTTTTGTTTTTTTTTTTTTTTTGGTTTTTCTTTTTTTCATTTTTTTTTTCT
1 TTTTTTTG-TTTGTTTTTGTTTTTTTTTTTTTTTTGGTTTTTCTTTTTTTCATTTTTTTTTTCT
* ** *
3668213 GGTTTTTCATTT-TTTTCGTTTTTTTTTTTTGTTTTGG
1 -TTTTTTTGTTTGTTTTTGTTTTTTTTTTTT-TTTTGG
3668250 AGGACGCCGT
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
63 17 0.19
64 16 0.18
65 26 0.29
66 28 0.31
67 2 0.02
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.84
Consensus pattern (63 bp):
TTTTTTTGTTTGTTTTTGTTTTTTTTTTTTTTTTGGTTTTTCTTTTTTTCATTTTTTTTTTCT
Found at i:3668219 original size:45 final size:45
Alignment explanation
Indices: 3668084--3668242 Score: 125
Period size: 45 Copynumber: 3.5 Consensus size: 45
3668074 CCGGACCCCC
*
3668084 TTTTTTT-GTTTGTT-TTTTTATTGTT-TTTTGTTTTTTGTTTTTTTTT
1 TTTTTTTCGTTT-TTCTTTTT-TT-TTGTTTTG-TTTTTGTGTTTTTTT
** *
3668130 TTTTGTTTTTTTTTTGCTTTTTTTTTGTTTTGTTTTTGTTTTTTTTT
1 TTTT-TTTCGTTTTT-CTTTTTTTTTGTTTTGTTTTTGTGTTTTTTT
* **
3668177 TTTTTTTGGTTTTTCTTTTTTTCATT-TTTT-TTTTCTG-GTTTTTCA
1 TTTTTTTCGTTTTTCTTTTTTT--TTGTTTTGTTTT-TGTGTTTTTTT
3668222 TTTTTTTCGTTTTT-TTTTTTT
1 TTTTTTTCGTTTTTCTTTTTTT
3668243 GTTTTGGAGG
Statistics
Matches: 98, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
44 7 0.07
45 30 0.31
46 18 0.18
47 28 0.29
48 10 0.10
49 5 0.05
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (45 bp):
TTTTTTTCGTTTTTCTTTTTTTTTGTTTTGTTTTTGTGTTTTTTT
Found at i:3680075 original size:52 final size:52
Alignment explanation
Indices: 3679995--3680114 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
3679985 AAAAGTTGTT
*
3679995 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
3680047 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
3680099 TGCATGTATCGATACA
1 TGCATGTATCGATACA
3680115 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:3680127 original size:52 final size:51
Alignment explanation
Indices: 3679995--3680134 Score: 210
Period size: 52 Copynumber: 2.7 Consensus size: 51
3679985 AAAAGTTGTT
3679995 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
* *
3680047 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
*
3680099 TGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3680135 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:3680141 original size:13 final size:13
Alignment explanation
Indices: 3680123--3680147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3680113 CAAAGATCAG
3680123 TGTATCGATACAA
1 TGTATCGATACAA
3680136 TGTATCGATACA
1 TGTATCGATACA
3680148 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3680229 original size:13 final size:13
Alignment explanation
Indices: 3680211--3680235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3680201 AAAAAAAATA
3680211 TGTATCGATACAT
1 TGTATCGATACAT
3680224 TGTATCGATACA
1 TGTATCGATACA
3680236 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3680334 original size:21 final size:21
Alignment explanation
Indices: 3680293--3680334 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3680283 GTTGGGACCT
*
3680293 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
3680314 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
3680335 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:3683618 original size:66 final size:64
Alignment explanation
Indices: 3683510--3683681 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 64
3683500 TAGGTTCCTT
* * *
3683510 ACAAAGCACACAAGCGAGCAACAAAGTTACCACGCATAAGTGCCACAAAACTAAAACAAGCTATC
1 ACAAAGCAAACAAGC-AGCAACTAAGTTGCCACGCATAAGTGCCACAAAACTAAAACAAGCTATC
* * *
3683575 ACAAAAGCAAACAAGCATGCAACTAGGTTGCCATGCATAAGTGCCACAAAACTAAAGCAAGCTAT
1 AC-AAAGCAAACAAGCA-GCAACTAAGTTGCCACGCATAAGTGCCACAAAACTAAAACAAGCTAT
*
3683640 T
64 C
* * *
3683641 ACAAGGCATACAAGTAAGCAACTAAGTTGCCACGCATAAGT
1 ACAAAGCAAACAAG-CAGCAACTAAGTTGCCACGCATAAGT
3683682 ACTACAGAGT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
65 35 0.38
66 57 0.62
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (64 bp):
ACAAAGCAAACAAGCAGCAACTAAGTTGCCACGCATAAGTGCCACAAAACTAAAACAAGCTATC
Found at i:3686670 original size:21 final size:21
Alignment explanation
Indices: 3686641--3686683 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3686631 TCACCAGCCT
* *
3686641 TGGTTGACATAAATCGATTCC
1 TGGTCGACATAAACCGATTCC
*
3686662 TGGTCGACATAAACCTATTCC
1 TGGTCGACATAAACCGATTCC
3686683 T
1 T
3686684 AGTTCTATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (21 bp):
TGGTCGACATAAACCGATTCC
Found at i:3689219 original size:11 final size:12
Alignment explanation
Indices: 3689205--3689238 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3689195 ATTATTACAT
3689205 AAATATAAT-TA
1 AAATATAATATA
3689216 AAATATAATATA
1 AAATATAATATA
*
3689228 AAAAATAATAT
1 AAATATAATAT
3689239 CAATACGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATAATATA
Found at i:3689329 original size:43 final size:44
Alignment explanation
Indices: 3689275--3689372 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 44
3689265 TTTAAATTTT
* * *
3689275 TATAACATAAATTAT-TAACA-TTTATATATATATATATATCAAAA
1 TATAATATAAATTATATAACATTTTATAT-TATA-AAATATAAAAA
*
3689319 T-TAATATAAA-TATATAATATTTTATATTATAAAATATAAAAA
1 TATAATATAAATTATATAACATTTTATATTATAAAATATAAAAA
3689361 TATAATATAAAT
1 TATAATATAAAT
3689373 AAACATATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
42 13 0.28
43 25 0.54
44 8 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (44 bp):
TATAATATAAATTATATAACATTTTATATTATAAAATATAAAAA
Found at i:3689331 original size:20 final size:19
Alignment explanation
Indices: 3689302--3689373 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 19
3689292 ACATTTATAT
*
3689302 ATATATATATATCAAAATTA
1 ATATAAATATAT-AAAATTA
*
3689322 ATATAAATATATAATATTTTA
1 ATATAAATATATAA-A-ATTA
3689343 TATTATAAA-ATATAAAAATATA
1 -A-TATAAATATAT-AAAAT-TA
3689365 ATATAAATA
1 ATATAAATA
3689374 AACATATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
19 2 0.05
20 18 0.43
21 6 0.14
22 8 0.19
23 8 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATATATAAAATTA
Found at i:3689345 original size:32 final size:30
Alignment explanation
Indices: 3689309--3689368 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
3689299 TATATATATA
*
3689309 TATATCAAAATTAATATAAATATATAATATTT
1 TATATCAAAA--AATATAAAAATATAATATTT
* *
3689341 TATATTATAAAATATAAAAATATAATAT
1 TATATCAAAAAATATAAAAATATAATAT
3689369 AAATAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
32 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
TATATCAAAAAATATAAAAATATAATATTT
Found at i:3690155 original size:10 final size:10
Alignment explanation
Indices: 3690140--3690164 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3690130 TAAAAAATAA
3690140 TATTTAATTT
1 TATTTAATTT
3690150 TATTTAATTT
1 TATTTAATTT
3690160 TATTT
1 TATTT
3690165 GTTTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTAATTT
Found at i:3690685 original size:13 final size:15
Alignment explanation
Indices: 3690659--3690690 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3690649 ATAGTTTAAA
3690659 TAAAAATATAAAATT
1 TAAAAATATAAAATT
3690674 TAAAAA-AT-AAATT
1 TAAAAATATAAAATT
3690687 TAAA
1 TAAA
3690691 TAAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATATAAAATT
Found at i:3691074 original size:2 final size:2
Alignment explanation
Indices: 3691067--3691111 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3691057 CCATTGTACT
3691067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3691109 TA T
1 TA T
3691112 GTTTATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3691147 original size:24 final size:24
Alignment explanation
Indices: 3691127--3691183 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
3691117 TTTTTATATT
3691127 AATA-TAAAT-TTTAAAAATTATA
1 AATATTAAATATTTAAAAATTATA
* *
3691149 AATATTTAATATTTAAAAATTTTA
1 AATATTAAATATTTAAAAATTATA
3691173 AATATTAAATA
1 AATATTAAATA
3691184 AATAAGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 4 0.13
23 4 0.13
24 22 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AATATTAAATATTTAAAAATTATA
Found at i:3691150 original size:16 final size:16
Alignment explanation
Indices: 3691129--3691179 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3691119 TTTATATTAA
3691129 TATAAATTTTAAAAAT
1 TATAAATTTTAAAAAT
* *
3691145 TATAAATATTTAATATT
1 TATAAAT-TTTAAAAAT
* *
3691162 TAAAAATTTTAAATAT
1 TATAAATTTTAAAAAT
3691178 TA
1 TA
3691180 AATAAATAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAATTTTAAAAAT
Found at i:3691709 original size:20 final size:20
Alignment explanation
Indices: 3691672--3691710 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3691662 AATTATTTAT
3691672 ATTTTAAAACTTAATAAAAA
1 ATTTTAAAACTTAATAAAAA
*
3691692 ATTTATAAAA-TTACTAAAA
1 ATTT-TAAAACTTAATAAAA
3691711 TTAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTTAAAACTTAATAAAAA
Found at i:3692605 original size:27 final size:28
Alignment explanation
Indices: 3692575--3692631 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
3692565 TTGAATAATA
* * *
3692575 ATTTTAAAA-TGTTAAAATTACATTTAT
1 ATTTTAAAATTATTAAAATTAAAATTAT
3692602 A-TTTAAAATTATTAAAATTAAAATTAT
1 ATTTTAAAATTATTAAAATTAAAATTAT
3692629 ATT
1 ATT
3692632 AAATTATAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 7 0.28
27 17 0.68
28 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
ATTTTAAAATTATTAAAATTAAAATTAT
Found at i:3692720 original size:32 final size:32
Alignment explanation
Indices: 3692682--3692748 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
3692672 ATTACAAATT
*
3692682 ATATTATATAATATTATATAAAT-AA-TAATTAA
1 ATATTAT-TAATATT-TAAAAATAAATTAATTAA
*
3692714 ATATTATTTATATTTAAAAATAAATTAATTAA
1 ATATTATTAATATTTAAAAATAAATTAATTAA
3692746 ATA
1 ATA
3692749 AAATCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.19
31 8 0.26
32 17 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATATTATTAATATTTAAAAATAAATTAATTAA
Found at i:3693263 original size:15 final size:14
Alignment explanation
Indices: 3693232--3693308 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 14
3693222 TTCAATGATT
3693232 TTAAATTT-AA-T-
1 TTAAATTTAAATTA
3693243 TTAAATTTAAAATTA
1 TTAAATTT-AAATTA
3693258 TTAAATTTAAATTA
1 TTAAATTTAAATTA
3693272 TTTTTTAAATTTAAATTAA
1 ----TTAAATTTAAATT-A
* *
3693291 TTAATTTTATATTA
1 TTAAATTTAAATTA
3693305 TTAA
1 TTAA
3693309 CTTTCTAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
11 8 0.15
13 2 0.04
14 12 0.22
15 19 0.35
18 13 0.24
19 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAATTTAAATTA
Found at i:3693268 original size:32 final size:33
Alignment explanation
Indices: 3693231--3693305 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
3693221 ATTCAATGAT
3693231 TTTAAATT-TAATTTAAATTTAAAATT-ATTAAA
1 TTTAAATTATAATTTAAATTT-AAATTAATTAAA
** *
3693263 TTTAAATTATTTTTTAAATTTAAATTAATTAAT
1 TTTAAATTATAATTTAAATTTAAATTAATTAAA
*
3693296 TTTATATTAT
1 TTTAAATTAT
3693306 TAACTTTCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 13 0.35
33 24 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTAAATTATAATTTAAATTTAAATTAATTAAA
Found at i:3693282 original size:33 final size:33
Alignment explanation
Indices: 3693242--3693306 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3693232 TTAAATTTAA
3693242 TTTAAATTTAAAATT-ATTAAATTTAAATTATTT
1 TTTAAATTT-AAATTAATTAAATTTAAATTATTT
* *
3693275 TTTAAATTTAAATTAATTAATTTTATATTATT
1 TTTAAATTTAAATTAATTAAATTTAAATTATT
3693307 AACTTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTAAATTTAAATTAATTAAATTTAAATTATTT
Found at i:3693287 original size:18 final size:17
Alignment explanation
Indices: 3693242--3693289 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
3693232 TTAAATTTAA
3693242 TTTAAATTTAAA--ATT
1 TTTAAATTTAAATTATT
*
3693257 ATTAAATTTAAATTATTT
1 TTTAAATTTAAATTA-TT
3693275 TTTAAATTTAAATTA
1 TTTAAATTTAAATTA
3693290 ATTAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 11 0.39
17 1 0.04
18 16 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTATT
Found at i:3694509 original size:20 final size:18
Alignment explanation
Indices: 3694463--3694513 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
3694453 CATTGTGGTT
* *
3694463 AATAAATTAAAAAAATAG
1 AATAAAATAAAAAAACAG
3694481 AATATAAATAAAAAAACATG
1 AATA-AAATAAAAAAACA-G
3694501 AAGTAAAATAAAA
1 AA-TAAAATAAAA
3694514 GCATGCTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 11 0.39
21 2 0.07
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
AATAAAATAAAAAAACAG
Found at i:3694895 original size:22 final size:20
Alignment explanation
Indices: 3694853--3694900 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3694843 ATTAATATAA
* *
3694853 AATAATTTTTAAAATATTTT
1 AATATTTTTTAAAATAATTT
3694873 AATATTTTTTAAATAATAATTT
1 AATATTTTTT-AA-AATAATTT
3694895 AA-ATTT
1 AATATTT
3694901 ATAAATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 6 0.25
22 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTTTTTAAAATAATTT
Found at i:3695278 original size:2 final size:2
Alignment explanation
Indices: 3695273--3695304 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3695263 TTATGTTCAT
3695273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3695305 ATAATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3703822 original size:2 final size:2
Alignment explanation
Indices: 3703815--3703845 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3703805 ATGGCAATTT
3703815 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3703846 TTTCTGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3705019 original size:26 final size:26
Alignment explanation
Indices: 3704970--3705019 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3704960 ACTTTTGGTT
* *
3704970 AGAAAATTTAACTCTTGTATTTATTA
1 AGAAAATTTAACTATTGTACTTATTA
* *
3704996 AGAAAATTTAATTATTTTACTTAT
1 AGAAAATTTAACTATTGTACTTAT
3705020 ATTAGGTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (26 bp):
AGAAAATTTAACTATTGTACTTATTA
Found at i:3705407 original size:14 final size:15
Alignment explanation
Indices: 3705388--3705416 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3705378 TTTTTACATA
3705388 TAAAATAT-AAATAT
1 TAAAATATGAAATAT
3705402 TAAAATATGAAATAT
1 TAAAATATGAAATAT
3705417 ATTTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TAAAATATGAAATAT
Found at i:3706459 original size:2 final size:2
Alignment explanation
Indices: 3706454--3706479 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3706444 ATATATTTTA
3706454 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
3706480 GTTGTACTAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3706684 original size:16 final size:16
Alignment explanation
Indices: 3706663--3706718 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
3706653 TTTAATATAT
3706663 TTATATATTTATTAAA
1 TTATATATTTATTAAA
*
3706679 TTATAT-TTTAATT-AT
1 TTATATATTT-ATTAAA
*
3706694 TTTTATATTATATTAATA
1 TTATATATT-TATTAA-A
3706712 TTATATA
1 TTATATA
3706719 ATTGTACGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 9 0.29
16 14 0.45
17 2 0.06
18 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATATTTATTAAA
Found at i:3706686 original size:22 final size:21
Alignment explanation
Indices: 3706658--3706712 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
3706648 TAAATTTTAA
3706658 TATATTTATATATTTATTAAAT
1 TATATTTATATATTT-TTAAAT
*
3706680 TATATTT-TAATTATTTTTATAT
1 TATATTTAT-A-TATTTTTAAAT
*
3706702 TATATTAATAT
1 TATATTTATAT
3706713 TATATAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
21 2 0.07
22 20 0.71
23 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTTATATATTTTTAAAT
Found at i:3706687 original size:32 final size:32
Alignment explanation
Indices: 3706619--3706717 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
3706609 TTTATACTAA
* * * * *
3706619 ATTTTAATAAATTAATA-ATTTATATCACTTAA
1 ATTTTAATATATTTATATATTTAT-TAAATTAT
3706651 ATTTTAATATATTTATATATTTATTAAATTAT
1 ATTTTAATATATTTATATATTTATTAAATTAT
*
3706683 ATTTTAAT-TATTTTTATATTATATTAATATTAT
1 ATTTTAATATATTTATATATT-TATTAA-ATTAT
3706716 AT
1 AT
3706718 AATTGTACGG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 11 0.19
32 34 0.59
33 13 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTTTAATATATTTATATATTTATTAAATTAT
Found at i:3706693 original size:11 final size:11
Alignment explanation
Indices: 3706651--3706707 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
3706641 TATCACTTAA
3706651 ATTTTAA-TAT
1 ATTTTAATTAT
3706661 ATTTATATATT-T
1 ATTT-TA-ATTAT
*
3706673 A-TTAAATTAT
1 ATTTTAATTAT
3706683 ATTTTAATTAT
1 ATTTTAATTAT
3706694 -TTTTATATTAT
1 ATTTTA-ATTAT
3706705 ATT
1 ATT
3706708 AATATTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
9 3 0.08
10 12 0.32
11 17 0.45
12 5 0.13
13 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTTAATTAT
Found at i:3707506 original size:15 final size:16
Alignment explanation
Indices: 3707488--3707519 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3707478 ATTTATAAAA
3707488 AATAAATATA-TTAAT
1 AATAAATATATTTAAT
3707503 AATAAATATATTTAAT
1 AATAAATATATTTAAT
3707519 A
1 A
3707520 TTTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAAATATATTTAAT
Found at i:3708733 original size:18 final size:18
Alignment explanation
Indices: 3708705--3708743 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3708695 TATAAAGTAT
*
3708705 AATTATTAAAATATTATAA
1 AATTATTAAAAAATTA-AA
3708724 AATT-TTAAAAAATTAAA
1 AATTATTAAAAAATTAAA
3708741 AAT
1 AAT
3708744 AATATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATTAAAAAATTAAA
Found at i:3708762 original size:26 final size:25
Alignment explanation
Indices: 3708732--3708782 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
3708722 AAAATTTTAA
3708732 AAAATTAAAAATAATATATAATTATT
1 AAAATTAAAAATAATA-ATAATTATT
** *
3708758 AAAATTTTAAATAATAATATTTATT
1 AAAATTAAAAATAATAATAATTATT
3708783 TTTAATACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAATTAAAAATAATAATAATTATT
Found at i:3708787 original size:28 final size:28
Alignment explanation
Indices: 3708712--3708787 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
3708702 TATAATTATT
* *
3708712 AAAATATTATA-AAATTTTAAAAAATTA
1 AAAATAATATATAATTTTTAAAAAATTA
* **
3708739 AAAATAATATATAATTATTAAAATTTTA
1 AAAATAATATATAATTTTTAAAAAATTA
*
3708767 AATAATAATAT-TTATTTTTAA
1 AA-AATAATATATAATTTTTAA
3708788 TACTCATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 10 0.25
28 22 0.55
29 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAATAATATATAATTTTTAAAAAATTA
Found at i:3708920 original size:12 final size:12
Alignment explanation
Indices: 3708903--3708935 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3708893 TTTTTTTTAT
*
3708903 TTTTTAATAAAA
1 TTTTTAAAAAAA
3708915 TTTTTAAAAAAA
1 TTTTTAAAAAAA
3708927 -TTTTAAAAA
1 TTTTTAAAAA
3708936 TTAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTTTTAAAAAAA
Found at i:3709050 original size:24 final size:24
Alignment explanation
Indices: 3709013--3709082 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
3709003 GTAAATATTA
*
3709013 ATATATTATATATTGGTATTAT-CT
1 ATATATTATATATT-ATATTATACT
*
3709037 ATATATTA-ATTATTATATTATATT
1 ATATATTATA-TATTATATTATACT
*
3709061 ATATATTTTATATTATTATTAT
1 ATATATTATATATTA-TATTAT
3709083 TTTTATCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.18
24 25 0.64
25 7 0.18
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (24 bp):
ATATATTATATATTATATTATACT
Found at i:3709055 original size:12 final size:13
Alignment explanation
Indices: 3709007--3709079 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
3708997 TATTATGTAA
*
3709007 ATATTAATATATT
1 ATATTATTATATT
*
3709020 ATA-TATTGGTATT
1 ATATTATT-ATATT
*
3709033 AT-CTA-TATATT
1 ATATTATTATATT
3709044 A-ATTATTATATT
1 ATATTATTATATT
*
3709056 ATATTATATATTTT
1 ATATTAT-TATATT
3709070 ATATTATTAT
1 ATATTATTAT
3709080 TATTTTTATC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
11 7 0.14
12 11 0.22
13 19 0.39
14 12 0.24
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (13 bp):
ATATTATTATATT
Found at i:3709058 original size:17 final size:16
Alignment explanation
Indices: 3709038--3709082 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
3709028 GTATTATCTA
3709038 TATATTAATTATTATAT
1 TATATT-ATTATTATAT
*
3709055 TATATTA-TA-TATTT
1 TATATTATTATTATAT
3709069 TATATTATTATTAT
1 TATATTATTATTAT
3709083 TTTTATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 11 0.44
15 4 0.16
16 4 0.16
17 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTATTATTATAT
Found at i:3709088 original size:17 final size:16
Alignment explanation
Indices: 3709007--3709085 Score: 65
Period size: 17 Copynumber: 5.0 Consensus size: 16
3708997 TATTATGTAA
* *
3709007 ATATTAATA-TATTAT
1 ATATTATTATTATTTT
** *
3709022 ATATTGGTATTATCTAT
1 ATATTATTATTAT-TTT
*
3709039 ATATTAATTATTATATT
1 ATATT-ATTATTATTTT
3709056 ATATTA-TA-TATTTT
1 ATATTATTATTATTTT
3709070 ATATTATTATTATTTT
1 ATATTATTATTATTTT
3709086 TATCAAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
14 11 0.21
15 11 0.21
16 10 0.19
17 14 0.27
18 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (16 bp):
ATATTATTATTATTTT
Found at i:3710546 original size:16 final size:17
Alignment explanation
Indices: 3710517--3710550 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3710507 AGAAAGATGG
3710517 AAAGAAAAAAAAAGAAA
1 AAAGAAAAAAAAAGAAA
*
3710534 AAAG-AAAAGAAAGAAA
1 AAAGAAAAAAAAAGAAA
3710550 A
1 A
3710551 TGAGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAGAAA
Found at i:3711132 original size:11 final size:11
Alignment explanation
Indices: 3711113--3711150 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
3711103 TTTATTTGAT
3711113 AAAAAAAGAAA
1 AAAAAAAGAAA
*
3711124 AAGAAAAGAAA
1 AAAAAAAGAAA
3711135 AAAAAAAGAGAA
1 AAAAAAAGA-AA
3711147 AAAA
1 AAAA
3711151 TTTATGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:3711137 original size:18 final size:18
Alignment explanation
Indices: 3711113--3711148 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3711103 TTTATTTGAT
*
3711113 AAAAAAAGAAAAAGAAAAG
1 AAAAAAA-AAAGAGAAAAG
3711132 AAAAAAAAAAGAGAAAA
1 AAAAAAAAAAGAGAAAA
3711149 AATTTATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAGAAAAG
Found at i:3711653 original size:19 final size:18
Alignment explanation
Indices: 3711607--3711653 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3711597 TTATTTTACA
3711607 TAATTT-ATCATAATATTT
1 TAATTTAAT-ATAATATTT
3711625 TAATTTAATATAA-ATTT
1 TAATTTAATATAATATTT
3711642 TATATGTTAATA
1 TA-AT-TTAATA
3711654 ATATGTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.23
18 12 0.46
19 8 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTTAATATAATATTT
Found at i:3711827 original size:32 final size:35
Alignment explanation
Indices: 3711778--3711869 Score: 95
Period size: 37 Copynumber: 2.7 Consensus size: 35
3711768 TTTTATGTGT
* *
3711778 TTATATTTATA-AT-TTTTTGTAT-TTAA-AA-TA
1 TTATATTTTTATATATTTTTATATCTTAATAACTA
3711808 TTATATTTTTATATATTTTTTATATCTTAATAACTTA
1 TTATATTTTTATATA-TTTTTATATCTTAATAAC-TA
*
3711845 TTTTATTTTATATATATTTTTATAT
1 TTATATTTT-TATATATTTTTATAT
3711870 ATAATTTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
30 10 0.20
31 2 0.04
33 8 0.16
34 4 0.08
35 2 0.04
37 19 0.37
38 6 0.12
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (35 bp):
TTATATTTTTATATATTTTTATATCTTAATAACTA
Found at i:3711829 original size:11 final size:10
Alignment explanation
Indices: 3711809--3711871 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
3711799 TTTAAAATAT
3711809 TATATTTTTA
1 TATATTTTTA
3711819 TATATTTTT-
1 TATATTTTTA
* *
3711828 TATATCTTAA
1 TATATTTTTA
3711838 TA-ACTTATTT-
1 TATA-TT-TTTA
*
3711848 TAT-TTTATA
1 TATATTTTTA
3711857 TATATTTTTA
1 TATATTTTTA
3711867 TATAT
1 TATAT
3711872 AATTTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
8 2 0.05
9 13 0.32
10 24 0.59
11 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TATATTTTTA
Found at i:3711857 original size:34 final size:34
Alignment explanation
Indices: 3711777--3711857 Score: 78
Period size: 34 Copynumber: 2.4 Consensus size: 34
3711767 TTTTTATGTG
*
3711777 TTTATATTTATAATTTTTTGTATTTAAAATATTATA
1 TTTAT-TTTAT-ATTTTTTATATTTAAAATATTATA
* *
3711813 TTT-TTATATATTTTTTATATCTTAATAA-CTTAT-
1 TTTATTTTATATTTTTTATAT-TTAA-AATATTATA
3711846 TTTATTTTATAT
1 TTTATTTTATAT
3711858 ATATTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
33 13 0.34
34 19 0.50
35 3 0.08
36 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (34 bp):
TTTATTTTATATTTTTTATATTTAAAATATTATA
Found at i:3711864 original size:16 final size:15
Alignment explanation
Indices: 3711846--3711887 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
3711836 AATAACTTAT
3711846 TTTATTTTATATATA
1 TTTATTTTATATATA
*
3711861 TTT-TTATATATA-A
1 TTTATTTTATATATA
3711874 TTTATTTTATATAT
1 TTTATTTTATATAT
3711888 GGGAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTTTATATATA
Found at i:3713074 original size:4 final size:4
Alignment explanation
Indices: 3713065--3713094 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3713055 ATGTGGTGGA
3713065 AAAG AAAG AAAG AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
3713095 AAAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3713273 original size:11 final size:12
Alignment explanation
Indices: 3713246--3713271 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3713236 ATTTTAAGAG
3713246 TTTATATTTTTA
1 TTTATATTTTTA
3713258 TTTATATTTTTA
1 TTTATATTTTTA
3713270 TT
1 TT
3713272 ATTTAAAATA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATATTTTTA
Found at i:3715528 original size:2 final size:2
Alignment explanation
Indices: 3715521--3715558 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3715511 ATGCTTCATA
3715521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3715559 TGTCAGTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3716591 original size:16 final size:17
Alignment explanation
Indices: 3716547--3716603 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
3716537 TTAACTTAAG
3716547 AAAATTTAAATAAAAATAT
1 AAAATTT-AATAAAAA-AT
*
3716566 TAAA-TT--TAAAAAAT
1 AAAATTTAATAAAAAAT
3716580 -AAATTTAATAAAAAAT
1 AAAATTTAATAAAAAAT
3716596 AAAATTTA
1 AAAATTTA
3716604 TTTAAAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 6 0.18
16 8 0.24
17 7 0.21
18 2 0.06
19 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTTAATAAAAAAT
Found at i:3716610 original size:17 final size:17
Alignment explanation
Indices: 3716569--3716612 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3716559 AAAATATTAA
3716569 ATTTAAAAAATAAATTT
1 ATTTAAAAAATAAATTT
*
3716586 A-ATAAAAAATAAAATTT
1 ATTTAAAAAAT-AAATTT
3716603 ATTTAAAAAA
1 ATTTAAAAAA
3716613 GAACTAAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTAAAAAATAAATTT
Found at i:3716824 original size:15 final size:15
Alignment explanation
Indices: 3716798--3716836 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
3716788 TAAAATTTAA
3716798 TAAAAAATATTAAAT
1 TAAAAAATATTAAAT
3716813 TATAAAAA-ATTAAAT
1 TA-AAAAATATTAAAT
3716828 TAAAAAATA
1 TAAAAAATA
3716837 AAATATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 12 0.55
16 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAAATATTAAAT
Found at i:3716838 original size:12 final size:13
Alignment explanation
Indices: 3716789--3716845 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
3716779 TTTATATTTT
* *
3716789 AAAATTTAATAAA
1 AAAATTAAATTAA
3716802 AAATATTAAATTATAA
1 AAA-ATTAAA-T-TAA
3716818 AAAATTAAATTAA
1 AAAATTAAATTAA
*
3716831 AAAATAAAATATAA
1 AAAATTAAAT-TAA
3716845 A
1 A
3716846 CGAATGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 15 0.41
14 10 0.27
15 7 0.19
16 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAATTAA
Found at i:3717537 original size:6 final size:6
Alignment explanation
Indices: 3717526--3717560 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
3717516 AAGTTCTTGG
3717526 AAGAAA AAGAAA AAGAAA AAG-AA AAG-AA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A
3717561 GTGTCAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:3723452 original size:30 final size:33
Alignment explanation
Indices: 3723372--3723452 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 33
3723362 AAAATAATTT
*
3723372 TTAAAAAATATTA-A-TATGTAATTATTATTTA
1 TTAAAAAATATTATATTATGTAATTATTATTAA
3723403 -TAAAAAATATTACATATTAT-T-ATT-TTATTAA
1 TTAAAAAATATT--ATATTATGTAATTATTATTAA
3723434 TTAAAAAATATTATATTAT
1 TTAAAAAATATTATATTAT
3723453 CGTTATTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
30 18 0.41
31 6 0.14
32 15 0.34
33 2 0.05
34 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
TTAAAAAATATTATATTATGTAATTATTATTAA
Found at i:3723615 original size:24 final size:24
Alignment explanation
Indices: 3723588--3723671 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
3723578 CAAAAAATAA
*
3723588 AAGAAAAGAGAGCAGAAGG-GAGAG
1 AAGAAAA-AGAGGAGAAGGAGAGAG
* *
3723612 AAGAAAAAGAGGGGAAAGGAAAGAG
1 AAGAAAAAGAGGAG-AAGGAGAGAG
3723637 AAGAGAAAAGAGGAG-AGGAGAGAG
1 AAGA-AAAAGAGGAGAAGGAGAGAG
3723661 AAGAAAAAGAG
1 AAGAAAAAGAG
3723672 AGGGTGACTG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 12 0.23
24 23 0.44
25 8 0.15
26 9 0.17
ACGTcount: A:0.58, C:0.01, G:0.40, T:0.00
Consensus pattern (24 bp):
AAGAAAAAGAGGAGAAGGAGAGAG
Found at i:3723980 original size:9 final size:9
Alignment explanation
Indices: 3723956--3724004 Score: 50
Period size: 8 Copynumber: 5.8 Consensus size: 9
3723946 ATTCGTAAGT
3723956 AAAA-AGAA
1 AAAATAGAA
*
3723964 TAAA-AGAA
1 AAAATAGAA
3723972 AAAATAGAA
1 AAAATAGAA
* *
3723981 AAAAAATAA
1 AAAATAGAA
3723990 AAAATA-AA
1 AAAATAGAA
3723998 AAAATAG
1 AAAATAG
3724005 TTGTTTTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (9 bp):
AAAATAGAA
Found at i:3723985 original size:17 final size:17
Alignment explanation
Indices: 3723956--3724001 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
3723946 ATTCGTAAGT
*
3723956 AAAA-AGAATAAAAGAA
1 AAAATAGAAAAAAAGAA
*
3723972 AAAATAGAAAAAAAATAA
1 AAAATAG-AAAAAAAGAA
3723990 AAAATA-AAAAAA
1 AAAATAGAAAAAA
3724002 TAGTTGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 10 0.38
17 2 0.08
18 14 0.54
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAAAAGAA
Found at i:3723991 original size:18 final size:17
Alignment explanation
Indices: 3723965--3724001 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3723955 TAAAAAGAAT
3723965 AAAAGAAAAAATAGAAAA
1 AAAAGAAAAAATA-AAAA
*
3723983 AAAATAAAAAATAAAAA
1 AAAAGAAAAAATAAAAA
3724000 AA
1 AA
3724002 TAGTTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.08
Consensus pattern (17 bp):
AAAAGAAAAAATAAAAA
Found at i:3724518 original size:21 final size:20
Alignment explanation
Indices: 3724482--3724521 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3724472 ATTGCAATTT
3724482 TTGTTTTTTTTCTATTATTA
1 TTGTTTTTTTTCTATTATTA
*
3724502 TTGTTTTATTTTTTATTATT
1 TTGTTTT-TTTTCTATTATT
3724522 TACCATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.78
Consensus pattern (20 bp):
TTGTTTTTTTTCTATTATTA
Found at i:3730248 original size:17 final size:17
Alignment explanation
Indices: 3730226--3730260 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3730216 TGTGCCTACA
3730226 CATCGTCTTAGCAAAGG
1 CATCGTCTTAGCAAAGG
3730243 CATCGTCTTAGCAAAGG
1 CATCGTCTTAGCAAAGG
3730260 C
1 C
3730261 GCATTCTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (17 bp):
CATCGTCTTAGCAAAGG
Found at i:3730295 original size:15 final size:15
Alignment explanation
Indices: 3730275--3730304 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3730265 TCTCTGGAGG
*
3730275 TTGGTATGGATTTTT
1 TTGGTATAGATTTTT
3730290 TTGGTATAGATTTTT
1 TTGGTATAGATTTTT
3730305 ACTGGGAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (15 bp):
TTGGTATAGATTTTT
Found at i:3730799 original size:88 final size:88
Alignment explanation
Indices: 3730687--3730850 Score: 238
Period size: 88 Copynumber: 1.9 Consensus size: 88
3730677 TAAAAAATAG
* * *
3730687 AATAGCGAAAAGGAAATTACCTGTGACTTAAGCAAATATACACGCATAAACTATTATACATTGAA
1 AATAGCGAAAAGGAAATTACCTGTGACTTAAGCAAATACACACACATAAACTATTATACATTCAA
*
3730752 AATAAGGAATAGTAGCCAAAGAT
66 AACAAGGAATAGTAGCCAAAGAT
* * ** * *
3730775 AATAGTGAAAAGGAAATTATCTGTGACTTAAGTGAATACACACATATAAATTATTATACATTCAA
1 AATAGCGAAAAGGAAATTACCTGTGACTTAAGCAAATACACACACATAAACTATTATACATTCAA
3730840 AACAAGGAATA
66 AACAAGGAATA
3730851 TCAAATAACA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 66 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (88 bp):
AATAGCGAAAAGGAAATTACCTGTGACTTAAGCAAATACACACACATAAACTATTATACATTCAA
AACAAGGAATAGTAGCCAAAGAT
Found at i:3731941 original size:25 final size:28
Alignment explanation
Indices: 3731913--3731963 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
3731903 CAATCGATCG
3731913 ATTTT-AAATA-ATTTATA-TTATATAA
1 ATTTTAAAATATATTTATATTTATATAA
*
3731938 ATTTTAAAATATTTTTATATTTATAT
1 ATTTTAAAATATATTTATATTTATAT
3731964 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 5 0.23
27 6 0.27
28 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTTAAAATATATTTATATTTATATAA
Found at i:3731969 original size:15 final size:17
Alignment explanation
Indices: 3731949--3731982 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3731939 TTTTAAAATA
3731949 TTTTTA-TAT-TTATAT
1 TTTTTATTATATTATAT
3731964 TTTTTATTATATTATAT
1 TTTTTATTATATTATAT
3731981 TT
1 TT
3731983 AATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATTATATTATAT
Found at i:3731975 original size:12 final size:12
Alignment explanation
Indices: 3731946--3732010 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
3731936 AAATTTTAAA
3731946 ATATTTTTATATTT
1 ATATTTTT-TA-TT
3731960 ATATTTTTTATT
1 ATATTTTTTATT
* *
3731972 ATATTATAT-TT
1 ATATTTTTTATT
*
3731983 A-ATTTTTTATC
1 ATATTTTTTATT
3731994 ATA-TTTTTATTT
1 ATATTTTTTA-TT
3732006 ATATT
1 ATATT
3732011 GTAAAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
10 5 0.12
11 11 0.27
12 14 0.34
13 3 0.07
14 8 0.20
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTTTTTATT
Found at i:3731982 original size:23 final size:24
Alignment explanation
Indices: 3731951--3732010 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
3731941 TTAAAATATT
*
3731951 TTTATATTTATATTTTTTATTATA
1 TTTATATTTATATTTTTTATCATA
3731975 -TTATATTTA-ATTTTTTATCATA
1 TTTATATTTATATTTTTTATCATA
*
3731997 TTTTTATTTATATT
1 TTTATATTTATATT
3732011 GTAAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 12 0.38
23 17 0.53
24 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATATTTATATTTTTTATCATA
Found at i:3732743 original size:19 final size:18
Alignment explanation
Indices: 3732702--3732739 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3732692 GACTCATGCC
3732702 AATTTGTAATTAGTCAAA
1 AATTTGTAATTAGTCAAA
3732720 AATTTGTAATTAGTCAAA
1 AATTTGTAATTAGTCAAA
3732738 AA
1 AA
3732740 ATTTCTTCTT
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:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (18 bp):
AATTTGTAATTAGTCAAA
Found at i:3735012 original size:15 final size:15
Alignment explanation
Indices: 3734992--3735022 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3734982 AATACTCAAG
3734992 TTTTATTATTATTAT
1 TTTTATTATTATTAT
*
3735007 TTTTATTTTTATTAT
1 TTTTATTATTATTAT
3735022 T
1 T
3735023 ATTGTATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTATTATTAT
Found at i:3735321 original size:22 final size:22
Alignment explanation
Indices: 3735296--3735369 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 22
3735286 ATAATAAAAA
*
3735296 TTAAATTTAACTCATAAATTAT
1 TTAAATTAAACTCATAAATTAT
* * *
3735318 TTAAATTAAAAT-TTAAAATAT
1 TTAAATTAAACTCATAAATTAT
* * *
3735339 TTAAATTCAACTCACATAATAAT
1 TTAAATTAAACTCATA-AATTAT
3735362 TTAAATTA
1 TTAAATTA
3735370 TTCTAACTAA
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
21 17 0.44
22 11 0.28
23 11 0.28
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAATTAAACTCATAAATTAT
Found at i:3735394 original size:11 final size:11
Alignment explanation
Indices: 3735378--3735402 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3735368 TATTCTAACT
3735378 AATAAATAATC
1 AATAAATAATC
3735389 AATAAATAATC
1 AATAAATAATC
3735400 AAT
1 AAT
3735403 TTTTTAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATAATC
Found at i:3736343 original size:19 final size:19
Alignment explanation
Indices: 3736319--3736366 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
3736309 TTTCCGTCGC
3736319 ATGTTTCTGATAACTTTTG
1 ATGTTTCTGATAACTTTTG
3736338 ATGTTTCTGATAACTTTTG
1 ATGTTTCTGATAACTTTTG
3736357 ATGTTTCTGA
1 ATGTTTCTGA
3736367 ATTTATTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (19 bp):
ATGTTTCTGATAACTTTTG
Found at i:3736845 original size:21 final size:18
Alignment explanation
Indices: 3736819--3736862 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3736809 TATGTAATAA
3736819 ATTTATAATTTGAATTTTAAT
1 ATTTATAATTT---TTTTAAT
*
3736840 ATTTATGATTTTTTTAAT
1 ATTTATAATTTTTTTAAT
3736858 ATTTA
1 ATTTA
3736863 CTTATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
21 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTTATAATTTTTTTAAT
Found at i:3739070 original size:17 final size:17
Alignment explanation
Indices: 3739037--3739080 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3739027 TAAATCATTA
3739037 AAAATAA-TATATTTAAT
1 AAAATAATTAT-TTTAAT
3739054 ATAAA-AATTATTTTAAT
1 A-AAATAATTATTTTAAT
3739071 AAAATAATTA
1 AAAATAATTA
3739081 AATAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATTATTTTAAT
Found at i:3739794 original size:2 final size:2
Alignment explanation
Indices: 3739787--3739811 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3739777 GAATGTGAGT
3739787 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3739812 TCAACTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3739988 original size:77 final size:77
Alignment explanation
Indices: 3739894--3740049 Score: 240
Period size: 77 Copynumber: 2.0 Consensus size: 77
3739884 TCAAGAAAAT
* * * * ** *
3739894 TTTTATGATTATAATTATAATTTTTATATTTTTTAATAAGTTAATACAGAAATTCATGATTTTTA
1 TTTTATGATTATAATTATAATTATTATATTTTATAATAAGTTAATAAAAAAATTCATGACCTTAA
3739959 TGAATATAATAA
66 TGAATATAATAA
*
3739971 TTTTATGATTATGATTATAATTATTATATTTTATAATAAGTTAATAAAAAAATTCATGACCTTAA
1 TTTTATGATTATAATTATAATTATTATATTTTATAATAAGTTAATAAAAAAATTCATGACCTTAA
3740036 TGAATATAATAA
66 TGAATATAATAA
3740048 TT
1 TT
3740050 ACAATAATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (77 bp):
TTTTATGATTATAATTATAATTATTATATTTTATAATAAGTTAATAAAAAAATTCATGACCTTAA
TGAATATAATAA
Found at i:3741493 original size:20 final size:21
Alignment explanation
Indices: 3741468--3741506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3741458 AATTAGATTG
3741468 TATTTAA-ATTTTTAAAATTT
1 TATTTAATATTTTTAAAATTT
*
3741488 TATTTAATTTTTTTAAAAT
1 TATTTAATATTTTTAAAAT
3741507 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTAATATTTTTAAAATTT
Found at i:3741592 original size:16 final size:16
Alignment explanation
Indices: 3741558--3741590 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3741548 TAAAATTAAA
3741558 TTAAATTATATAAAAT
1 TTAAATTATATAAAAT
*
3741574 TTAAATTTTA-AAAAT
1 TTAAATTATATAAAAT
3741589 TT
1 TT
3741591 TATTTAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATTATATAAAAT
Found at i:3742908 original size:24 final size:24
Alignment explanation
Indices: 3742880--3742934 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3742870 ATCAAAATTA
3742880 TAAATATA-AATA-TAATATATATGT
1 TAAATATATAATATTAAT-TATAT-T
*
3742904 TAAATATATTATATTAATTATATT
1 TAAATATATAATATTAATTATATT
3742928 TAAATAT
1 TAAATAT
3742935 GTTACATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 16 0.57
25 8 0.29
26 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAAATATATAATATTAATTATATT
Found at i:3743824 original size:2 final size:2
Alignment explanation
Indices: 3743812--3743844 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3743802 TAATCTTGTG
*
3743812 AT AT TT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3743845 TTTATAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:3745526 original size:7 final size:7
Alignment explanation
Indices: 3745514--3745547 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3745504 ACAATAATAA
3745514 AAATTTT
1 AAATTTT
3745521 AAATTTT
1 AAATTTT
3745528 AAA-TTT
1 AAATTTT
3745534 AAATTTT
1 AAATTTT
3745541 AATATTT
1 AA-ATTT
3745548 ACCATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 15 0.60
8 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AAATTTT
Found at i:3745536 original size:13 final size:14
Alignment explanation
Indices: 3745518--3745548 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3745508 TAATAAAAAT
3745518 TTTAAATTTTAA-A
1 TTTAAATTTTAATA
3745531 TTTAAATTTTAATA
1 TTTAAATTTTAATA
3745545 TTTA
1 TTTA
3745549 CCATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAAATTTTAATA
Found at i:3745628 original size:2 final size:2
Alignment explanation
Indices: 3745621--3745646 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3745611 AACCTAACCC
3745621 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3745647 CACTTTTCCA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3745917 original size:23 final size:25
Alignment explanation
Indices: 3745891--3745937 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3745881 TTAATTTAAT
3745891 TAATTTAT-ATA-ATTATTTAAAAA
1 TAATTTATAATATATTATTTAAAAA
* *
3745914 TAATTTTTAATATATTTTTTAAAA
1 TAATTTATAATATATTATTTAAAA
3745938 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 3 0.15
25 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TAATTTATAATATATTATTTAAAAA
Found at i:3745926 original size:26 final size:26
Alignment explanation
Indices: 3745897--3745951 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3745887 TAATTAATTT
*
3745897 ATATAATTATTTAAAA-ATAATTTTTA
1 ATAT-ATTATTTAAAATATAAATTTTA
* *
3745923 ATATATTTTTTAAAATTTAAATTTTA
1 ATATATTATTTAAAATATAAATTTTA
3745949 ATA
1 ATA
3745952 CTTATCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATATTATTTAAAATATAAATTTTA
Found at i:3746537 original size:41 final size:44
Alignment explanation
Indices: 3746475--3746575 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 44
3746465 GATATTTATA
* * * *
3746475 AAAAATTATATTTAATTAATATAT-TA-TTTTTT-AAAT-TTAAT
1 AAAAATAATATAT-ATTAATATATAAATTTTTTTAAAATAATAAT
3746516 AAAAATAATATATATTAAATATATAAATTTTTTTAAAAATAATAAT
1 AAAAATAATATATATT-AATATATAAATTTTTTT-AAAATAATAAT
*
3746562 AAAAATAATTTATA
1 AAAAATAATATATA
3746576 ATACTAGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
40 3 0.06
41 18 0.37
42 1 0.02
43 6 0.12
45 4 0.08
46 17 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (44 bp):
AAAAATAATATATATTAATATATAAATTTTTTTAAAATAATAAT
Found at i:3746649 original size:14 final size:14
Alignment explanation
Indices: 3746624--3746674 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
3746614 AATATTTTTT
*
3746624 TAATTTAATAAAAA
1 TAATATAATAAAAA
* *
3746638 TAATATATTAAATA
1 TAATATAATAAAAA
3746652 TAA-ATAAT-AAAA
1 TAATATAATAAAAA
3746664 TAATA-AATAAA
1 TAATATAATAAA
3746675 TAATCATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 9 0.30
13 7 0.23
14 14 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATATAATAAAAA
Found at i:3746670 original size:21 final size:20
Alignment explanation
Indices: 3746631--3746672 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3746621 TTTTAATTTA
* *
3746631 ATAAAAATAATATATTAAAT
1 ATAAAAATAAAATAATAAAT
3746651 ATAAATAATAAAATAATAAAT
1 ATAAA-AATAAAATAATAAAT
3746672 A
1 A
3746673 AATAATCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAAATAAAATAATAAAT
Found at i:3746685 original size:26 final size:27
Alignment explanation
Indices: 3746628--3746685 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
3746618 TTTTTTTAAT
*
3746628 TTAATAAAAATAATATATTAAATATAA
1 TTAATAAAAATAATATAATAAATATAA
* *
3746655 ATAAT-AAAATAATA-AATAAATAATCA
1 TTAATAAAAATAATATAATAAAT-ATAA
3746681 TTAAT
1 TTAAT
3746686 CAATATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 6 0.23
26 16 0.62
27 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
TTAATAAAAATAATATAATAAATATAA
Done.