Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008554.1 Hibiscus syriacus cultivar Beakdansim tig00111458_pilon, 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: 3217407
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2830852 original size:21 final size:21
Alignment explanation
Indices: 2830741--2830859 Score: 89
Period size: 21 Copynumber: 5.6 Consensus size: 21
2830731 ACCCCGTGGA
* *
2830741 GGGTATCGATACC-CTC-AGG
1 GGGTATCGATACCAATCAAAG
*
2830760 GGGTATCGATACCCATTCAAAG
1 GGGTATCGATA-CCAATCAAAG
* * * *
2830782 AGGGTATCGATGCCTATTATAG
1 -GGGTATCGATACCAATCAAAG
*
2830804 GGGTATCGATACCTATTCAAAGG
1 GGGTATCGATACC-AATCAAA-G
**
2830827 GGGTATCGATACCAATCTTAG
1 GGGTATCGATACCAATCAAAG
*
2830848 GGGTATTGATAC
1 GGGTATCGATAC
2830860 TCTATGCACA
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
19 11 0.14
20 2 0.03
21 26 0.33
22 15 0.19
23 24 0.31
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
GGGTATCGATACCAATCAAAG
Found at i:2836479 original size:21 final size:21
Alignment explanation
Indices: 2836448--2836547 Score: 118
Period size: 21 Copynumber: 4.9 Consensus size: 21
2836438 CCATTATATG
2836448 CCTGA-GGGGTATCGGTACCT
1 CCTGAGGGGGTATCGGTACCT
2836468 CCTGAGGGGGTATCGGTACCT
1 CCTGAGGGGGTATCGGTACCT
2836489 CCTGAGGGGGTATCGGTACCAT
1 CCTGAGGGGGTATCGGTACC-T
* * *
2836511 TC-AATGGGGGTATCGATACC-
1 CCTGA-GGGGGTATCGGTACCT
*
2836531 ACTG-GGGGGTATCGGTA
1 CCTGAGGGGGTATCGGTA
2836548 TCATCTGAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 12 0.17
20 6 0.09
21 36 0.51
22 16 0.23
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (21 bp):
CCTGAGGGGGTATCGGTACCT
Found at i:2836506 original size:42 final size:42
Alignment explanation
Indices: 2836448--2836552 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 42
2836438 CCATTATATG
* *
2836448 CCTGA-GGGGTATCGGTACC-TCCTGA-GGGGGTATCGGTACC
1 CCTGAGGGGGTATCGGTACCATCC-AATGGGGGTATCGATACC
*
2836488 TCCTGAGGGGGTATCGGTACCATTCAATGGGGGTATCGATACC
1 -CCTGAGGGGGTATCGGTACCATCCAATGGGGGTATCGATACC
* *
2836531 ACTG-GGGGGTATCGGTATCATC
1 CCTGAGGGGGTATCGGTACCATC
2836553 TGAGAATTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 21 0.38
42 18 0.33
43 16 0.29
ACGTcount: A:0.18, C:0.22, G:0.35, T:0.25
Consensus pattern (42 bp):
CCTGAGGGGGTATCGGTACCATCCAATGGGGGTATCGATACC
Found at i:2845122 original size:6 final size:6
Alignment explanation
Indices: 2845111--2845135 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2845101 ACACTTATAT
2845111 CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC C
2845136 TATGGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:2847156 original size:59 final size:57
Alignment explanation
Indices: 2847026--2847162 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 57
2847016 ATAAGCACCG
* * **
2847026 TAGTGCTATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCT
2847084 TA-TGTACAGTCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGT--A-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC-T
2847144 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
2847163 CAGCCTGCTG
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
56 1 0.01
57 2 0.03
58 3 0.04
59 57 0.83
60 3 0.04
61 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (57 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCT
Found at i:2854069 original size:29 final size:29
Alignment explanation
Indices: 2854036--2854094 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2854026 CATAAAGCCT
*
2854036 AAGAATATTAAAAAAGTATTAAATGATGA
1 AAGAATATTAAAAAAGCATTAAATGATGA
2854065 AAGAATATTAAAAAAGCATTAAATGATGA
1 AAGAATATTAAAAAAGCATTAAATGATGA
2854094 A
1 A
2854095 CATTGGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (29 bp):
AAGAATATTAAAAAAGCATTAAATGATGA
Found at i:2855442 original size:15 final size:15
Alignment explanation
Indices: 2855424--2855454 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2855414 GCATATTAAA
*
2855424 ATTAGACATCATTTC
1 ATTAGAAATCATTTC
2855439 ATTAGAAATCATTTC
1 ATTAGAAATCATTTC
2855454 A
1 A
2855455 CCAAAGGAGA
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:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (15 bp):
ATTAGAAATCATTTC
Found at i:2857027 original size:19 final size:19
Alignment explanation
Indices: 2856999--2857036 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2856989 ATTGATAAGG
*
2856999 GTTTAGGTGCTTCGAGATT
1 GTTTAAGTGCTTCGAGATT
*
2857018 GTTTAAGTGCTTTGAGATT
1 GTTTAAGTGCTTCGAGATT
2857037 TCTATGTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (19 bp):
GTTTAAGTGCTTCGAGATT
Found at i:2859185 original size:2 final size:2
Alignment explanation
Indices: 2859143--2859176 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2859133 CATTAAAACA
*
2859143 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2859177 CCTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2859373 original size:12 final size:13
Alignment explanation
Indices: 2859345--2859394 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
2859335 AACTTTCTTT
*
2859345 TTTCA-TTTCATC
1 TTTCATTTTCATA
*
2859357 TTTCACTTTCATA
1 TTTCATTTTCATA
*
2859370 -TTCATTTTCACA
1 TTTCATTTTCATA
2859382 TTTCATTTTCATA
1 TTTCATTTTCATA
2859395 ACCAATACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 15 0.47
13 17 0.53
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTCATTTTCATA
Found at i:2859378 original size:25 final size:24
Alignment explanation
Indices: 2859346--2859394 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2859336 ACTTTCTTTT
2859346 TTCATTTCATC-TTTCACTTTCATA
1 TTCATTTCA-CATTTCACTTTCATA
*
2859370 TTCATTTTCACATTTCATTTTCATA
1 TTCA-TTTCACATTTCACTTTCATA
2859395 ACCAATACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.55
Consensus pattern (24 bp):
TTCATTTCACATTTCACTTTCATA
Found at i:2859456 original size:19 final size:19
Alignment explanation
Indices: 2859427--2859477 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
2859417 ATTCATTTTC
*
2859427 GATTCAGAACTTATTTCCA
1 GATTCATAACTTATTTCCA
* *
2859446 TATTCATAACTTATTTTCA
1 GATTCATAACTTATTTCCA
2859465 GATTCATAACTTA
1 GATTCATAACTTA
2859478 AATTCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (19 bp):
GATTCATAACTTATTTCCA
Found at i:2859483 original size:19 final size:19
Alignment explanation
Indices: 2859447--2859491 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2859437 TTATTTCCAT
** *
2859447 ATTCATAACTTATTTTCAG
1 ATTCATAACTTAAATTCAA
2859466 ATTCATAACTTAAATTCAA
1 ATTCATAACTTAAATTCAA
2859485 ATTCATA
1 ATTCATA
2859492 CCCCAATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTCATAACTTAAATTCAA
Found at i:2864142 original size:59 final size:58
Alignment explanation
Indices: 2864008--2864144 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 58
2863998 ATAAGCACCG
* **
2864008 TAGTGCTATCCCGAATATGAACAATAAGGTCGTGCCCACCATCTGTACTAGATATCCTT
1 TAGTG-TATCCCGAATATGAACAATAAGGTCGTGCCCACCATATACACTAGATATCCTT
* ** * * *
2864067 AAGTACAGTCCTGAATATG-ACACATAAGGTCGTGCCTACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGAACA-ATAAGGTCGTGCCCACCATATACACTAGATATCCTT
2864126 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
2864145 CAGCCTACTG
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
58 4 0.06
59 58 0.94
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGAACAATAAGGTCGTGCCCACCATATACACTAGATATCCTT
Found at i:2866855 original size:361 final size:360
Alignment explanation
Indices: 2866192--2866916 Score: 1369
Period size: 361 Copynumber: 2.0 Consensus size: 360
2866182 CCCTAAACTT
2866192 TTCCCAAGTTTTATACTTTGACCATCAAACTTTTAAAAGTTTCATTTTAGTCATTGTTTAATTTT
1 TTCCCAAGTTTTATACTTTGACCATCAAACTTTTAAAAGTTTCATTTTAGTCATTGTTTAATTTT
* *
2866257 TTGGGGTATTACAATTCTCCCCTCTTTAGGAAAATTCGTCCTCGAATTTTCAGACTTTCTTTGAA
66 TTGGGGTATTACAATTCTCCCCTCCTTAGGAAAATTCATCCTCGAATTTTCAGACTTTCTTTGAA
*
2866322 AACCCTAACCCCCTTTTTATAAAGAATTTTATCAACAAAAATAAATCCCACCAAAATAGGGATTT
131 AACCCTAACCCCCTTTTTATAAAGAATTTTATAAACAAAAATAAATCCCACCAAAATAGGGATTT
*
2866387 TGTTTTACTGTCATCTTTCTCTAAAGATAAGAATACTTCAATAATATTTAAACCATCATTAGATT
196 TGTTTTACTGTCATATTTCTCTAAAGATAAGAATACTTCAATAATATTTAAACCATCATTAGATT
* *
2866452 CCTTTTTCCCTTGTACATTTGTAACCCTAATTTAGGGTTATACTGACTGGTAAGACTTAATCTCG
261 CCTTTTTCCCTTGTACATTCGTAACCCTAATTTAGGGTTATACTAACTGGTAAGACTTAATCTCG
2866517 TCTTATACAAAAACCTCTTCTGTCAACTTCTTGAA
326 TCTTATACAAAAACCTCTTCTGTCAACTTCTTGAA
2866552 TTCCCAAGTTTTATACTTTGACCATCAAACTTTTAAAAGTTTCATTTTAGTCATTGTTTAATTTT
1 TTCCCAAGTTTTATACTTTGACCATCAAACTTTTAAAAGTTTCATTTTAGTCATTGTTTAATTTT
*
2866617 TTGGGGTATTACAATTCTCCCCTCCTTAGGAAAATTCATCCTCGAATTTTTAGACTTTCTTTGAA
66 TTGGGGTATTACAATTCTCCCCTCCTTAGGAAAATTCATCCTCGAATTTTCAGACTTTCTTTGAA
2866682 AACCCTAACCTCCCTTTTTATAAAGAATTTTATAAACAAAAATAAATCCCACCAAAATAGGGATT
131 AACCCTAACC-CCCTTTTTATAAAGAATTTTATAAACAAAAATAAATCCCACCAAAATAGGGATT
2866747 TTGTTTTACTGTCATATTTCTCTAAAGATAAGAATACTTCAATAATATTTAAACCATCATTAGAT
195 TTGTTTTACTGTCATATTTCTCTAAAGATAAGAATACTTCAATAATATTTAAACCATCATTAGAT
*
2866812 TCCTTTTTCCCTTGTATATTCGTAACCCTAATTTAGGGTTATACTAACTGGTAAGACTTAATCTC
260 TCCTTTTTCCCTTGTACATTCGTAACCCTAATTTAGGGTTATACTAACTGGTAAGACTTAATCTC
2866877 GTCTTATACAAAAACCTCTTCTGTCAACTTCTTGAA
325 GTCTTATACAAAAACCTCTTCTGTCAACTTCTTGAA
2866913 TTCC
1 TTCC
2866917 GATTTTTTTT
Statistics
Matches: 356, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
360 137 0.38
361 219 0.62
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (360 bp):
TTCCCAAGTTTTATACTTTGACCATCAAACTTTTAAAAGTTTCATTTTAGTCATTGTTTAATTTT
TTGGGGTATTACAATTCTCCCCTCCTTAGGAAAATTCATCCTCGAATTTTCAGACTTTCTTTGAA
AACCCTAACCCCCTTTTTATAAAGAATTTTATAAACAAAAATAAATCCCACCAAAATAGGGATTT
TGTTTTACTGTCATATTTCTCTAAAGATAAGAATACTTCAATAATATTTAAACCATCATTAGATT
CCTTTTTCCCTTGTACATTCGTAACCCTAATTTAGGGTTATACTAACTGGTAAGACTTAATCTCG
TCTTATACAAAAACCTCTTCTGTCAACTTCTTGAA
Found at i:2868425 original size:13 final size:12
Alignment explanation
Indices: 2868401--2868442 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
2868391 GTGAATTTTT
2868401 TTTTCATTTCTCA
1 TTTTC-TTTCTCA
*
2868414 TTTT-TTTCTCTC
1 TTTTCTTTCTC-A
2868426 TTTTCTTTCTCA
1 TTTTCTTTCTCA
2868438 TTTTC
1 TTTTC
2868443 ATTTTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
13 10 0.40
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCTTTCTCA
Found at i:2868447 original size:28 final size:28
Alignment explanation
Indices: 2868416--2868477 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
2868406 ATTTCTCATT
2868416 TTTTTCTCTCTT-TTC-TTTCTCATTTTC
1 TTTTTCTCTCTTCTTCGTTT-TCATTTTC
*
2868443 ATTTTT-TTTCTTCTTCGTTTTCATTTTC
1 -TTTTTCTCTCTTCTTCGTTTTCATTTTC
2868471 TTTTTCT
1 TTTTTCT
2868478 ATTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 10 0.33
28 17 0.57
29 3 0.10
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTTTCTCTCTTCTTCGTTTTCATTTTC
Found at i:2868447 original size:30 final size:27
Alignment explanation
Indices: 2868396--2868512 Score: 93
Period size: 26 Copynumber: 4.3 Consensus size: 27
2868386 CATAAGTGAA
2868396 TTTTT-TTTTCATTTCTCATTTTTTTCTC
1 TTTTTCTTTTCATTT-TCATTTTTTT-TC
2868424 TCTTTTCTTTCTCATTTTCATTTTTTTTC
1 T-TTTTCTTT-TCATTTTCATTTTTTTTC
* * *
2868453 TTCTTCGTTTTCATTTTC--TTTTTCTA
1 TTTTTC-TTTTCATTTTCATTTTTTTTC
2868479 TTTTT-TTTTC-TTCTTC-TGTTTTTTTC
1 TTTTTCTTTTCATT-TTCAT-TTTTTTTC
*
2868505 TTCTTCTT
1 TTTTTCTT
2868513 ATAATATATA
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
23 2 0.03
24 8 0.11
26 20 0.27
27 2 0.03
28 13 0.18
29 10 0.14
30 13 0.18
31 6 0.08
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTTTCTTTTCATTTTCATTTTTTTTC
Found at i:2868451 original size:22 final size:23
Alignment explanation
Indices: 2868395--2868474 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 23
2868385 CCATAAGTGA
*
2868395 ATTTTTTTTTCATTTCTCATTTT-
1 ATTTTCTTTTC-TTTCTCATTTTC
*
2868418 TTTCTCTCTTTTCTTTCTCATTTTC
1 ATT-T-TCTTTTCTTTCTCATTTTC
*
2868443 ATTTT-TTTTC-TTCTTCGTTTTC
1 ATTTTCTTTTCTTTC-TCATTTTC
2868465 ATTTTCTTTT
1 ATTTTCTTTT
2868475 TCTATTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
21 3 0.06
22 17 0.35
23 7 0.15
24 13 0.27
25 8 0.17
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.72
Consensus pattern (23 bp):
ATTTTCTTTTCTTTCTCATTTTC
Found at i:2868484 original size:36 final size:34
Alignment explanation
Indices: 2868396--2868505 Score: 108
Period size: 31 Copynumber: 3.3 Consensus size: 34
2868386 CATAAGTGAA
*
2868396 TTTT-TTTTTCATTTCTCA-TTTTTTTC-TC-TC-
1 TTTTCTTTCTCATTT-TCATTTTTTTTCTTCTTCG
2868426 TTTTCTTTCTCATTTTCATTTTTTTTCTTCTTCG
1 TTTTCTTTCTCATTTTCATTTTTTTTCTTCTTCG
*
2868460 TTTTCATTT-TCTTTTTCTATTTTTTTTTCTTCTTCTG
1 TTTTC-TTTCTCATTTTC-A-TTTTTTTTCTTCTTC-G
2868497 TTTT-TTTCT
1 TTTTCTTTCT
2868506 TCTTCTTATA
Statistics
Matches: 68, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
30 7 0.10
31 17 0.25
32 2 0.03
33 2 0.03
34 12 0.18
35 7 0.10
36 16 0.24
37 5 0.07
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (34 bp):
TTTTCTTTCTCATTTTCATTTTTTTTCTTCTTCG
Found at i:2868500 original size:13 final size:13
Alignment explanation
Indices: 2868448--2868508 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 13
2868438 TTTTCATTTT
2868448 TTTTCTTCTTC-G
1 TTTTCTTCTTCTG
2868460 TTTTCATT-TTCT-
1 TTTTC-TTCTTCTG
*
2868472 TTTTCTAT-TT-TT
1 TTTTCT-TCTTCTG
2868484 TTTTCTTCTTCTG
1 TTTTCTTCTTCTG
*
2868497 TTTTTTTCTTCT
1 TTTTCTTCTTCT
2868509 TCTTATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 3 0.07
12 24 0.59
13 14 0.34
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTCTTCTTCTG
Found at i:2868501 original size:18 final size:18
Alignment explanation
Indices: 2868444--2868512 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
2868434 CTCATTTTCA
2868444 TTTTTTTTCTTCTTC-GT
1 TTTTTTTTCTTCTTCTGT
* * *
2868461 TTTCATTTTCTTTTTCTAT
1 TTT-TTTTTCTTCTTCTGT
2868480 TTTTTTTTCTTCTTCTGT
1 TTTTTTTTCTTCTTCTGT
2868498 TTTTTTCTTCTTCTT
1 TTTTTT-TTCTTCTT
2868513 ATAATATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.07
18 28 0.65
19 12 0.28
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTTTTCTTCTTCTGT
Found at i:2874871 original size:148 final size:148
Alignment explanation
Indices: 2874683--2874981 Score: 467
Period size: 148 Copynumber: 2.0 Consensus size: 148
2874673 AAACTATTTA
* *
2874683 AATTAGAATAAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACA-AAGACTCAA
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAA-ACTCAA
* *
2874747 AAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACTCAAATTGAAAAAATTTCA-AGTCAA
65 AAATTCAATTCAATTCGACTTGATTTAAATTTCATAAACACAAATCGAAAAAA-TTCAGAGTCAA
2874811 CTATTTTATAAACTGAACTG
129 CTATTTTATAAACTGAACTG
* * *
2874831 AATTATAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* * *
2874896 AATTCAATTCCATTCGACTTGATTTAAATTTTATAATCACAAATCGAAAAAATTCAGAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTCATAAACACAAATCGAAAAAATTCAGAGTCAACT
*
2874961 ATTTTATAAACTGAATTG
131 ATTTTATAAACTGAACTG
2874979 AAT
1 AAT
2874982 ATTTAGGTCC
Statistics
Matches: 138, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
147 4 0.03
148 132 0.96
149 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (148 bp):
AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAATTTCATAAACACAAATCGAAAAAATTCAGAGTCAACT
ATTTTATAAACTGAACTG
Found at i:2877762 original size:114 final size:114
Alignment explanation
Indices: 2877622--2878029 Score: 685
Period size: 114 Copynumber: 3.6 Consensus size: 114
2877612 GAAAGTATTT
* * * *
2877622 ATACTTTCAACTTATCACGTAGCTCTTTATCGGTTTTGTCATAATGAAACTGATTTTGTCATATT
1 ATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATT
2877687 TTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAATGATCG
66 TTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAATGATCG
2877736 ATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATT
1 ATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATT
* * *
2877801 TTCACCTGTTATATTGTAATGTATCGATACATTTTTATAAAAAGGATCG
66 TTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAATGATCG
*
2877850 ATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCACAATGAAACTGGTTTTGTCATATT
1 ATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATT
* * *
2877915 TTTACATGTTATATTGTAAAGTATCGATACCTTTTTAT-AAAGT-ATCG
66 TTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAATGATCG
* *
2877962 ATACTTTCAACATATCATGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGGTTTGTCATATT
1 ATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATT
2878027 TTT
66 TTT
2878030 TAATGACAAA
Statistics
Matches: 277, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
112 69 0.25
113 3 0.01
114 205 0.74
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (114 bp):
ATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATT
TTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAATGATCG
Found at i:2878939 original size:198 final size:199
Alignment explanation
Indices: 2878194--2878986 Score: 1221
Period size: 199 Copynumber: 4.0 Consensus size: 199
2878184 AATAAGTAAA
*
2878194 CATAAAGTATCGAT-CATTTTTAAAATTGTATTGATCCCAAGAACATCGAAACCTATAATTATAA
1 CATAAAGTATCGATACA--TTTAAAATTGTATCGATCCCAAGAACATCGAAACCTATAATTATAA
* * *
2878258 TCTAATAGGTAAATTTATAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTCTAC
64 TCTAATAGGTAAATTAACAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTAC
* *
2878323 ATAACGTATCAACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCTCAACGAGG
129 ATAATGTATCAACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGG
**
2878388 TGCAAT
194 TGCACG
* * * * * * *
2878394 CATAAAGTGTCGATACATTTAAAATTGTATCTATCCTAAAAATATCAAAACCTATAATTATAATG
1 CATAAAGTATCGATACATTTAAAATTGTATCGATCCCAAGAACATCGAAACCTATAATTATAATC
* * * * *
2878459 TAATAGGTAAATGAACGATGTAACAAATAGAAATATATCGGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTAACAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
* *
2878524 AATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGTCCAACGAGGTG
131 AATGTATCAACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTG
2878589 CACG
196 CACG
* *
2878593 CATAAAGTATCGATACATTTAAAATTGTATCGATGCCAAGAACATCGAAACATATAATTATAATC
1 CATAAAGTATCGATACATTTAAAATTGTATCGATCCCAAGAACATCGAAACCTATAATTATAATC
* *
2878658 TAATAGGTAAATTTACAATGTAACCAGTAGAAATATACCAGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTAACAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
* * * *
2878723 AATTTATCGACACTTTCTAAATTTCTGTCGATACTTTTTGTACAGAATGAATGCCCAACGAGGTG
131 AATGTATCAACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTG
2878788 CACG
196 CACG
* * *
2878792 CATAAAGTGTCGATACATTTAAAATTGTGTCGATCCCAA-AACATCGAAACCTATAATTATAATG
1 CATAAAGTATCGATACATTTAAAATTGTATCGATCCCAAGAACATCGAAACCTATAATTATAATC
* * *
2878856 TAATAGGTAAATTAACAATGCAACCAGTAGAAATATAGCGGTTTTATGAGAAAAAAGGTCTACAT
66 TAATAGGTAAATTAACAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
*
2878921 AATGTATCAACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATTAATGCCCAACGAGGTG
131 AATGTATCAACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTG
2878986 C
196 C
2878987 TTATTTTATT
Statistics
Matches: 535, Mismatches: 57, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
198 144 0.27
199 376 0.70
200 13 0.02
201 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
CATAAAGTATCGATACATTTAAAATTGTATCGATCCCAAGAACATCGAAACCTATAATTATAATC
TAATAGGTAAATTAACAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
AATGTATCAACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTG
CACG
Found at i:2879021 original size:23 final size:23
Alignment explanation
Indices: 2878995--2879044 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2878985 GCTTATTTTA
* *
2878995 TTATATAAGTGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
2879018 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
2879041 TTAT
1 TTAT
2879045 TGTGTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:2879098 original size:21 final size:21
Alignment explanation
Indices: 2879072--2879113 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2879062 CCAGTAATTA
**
2879072 ACCTATTTTATTATATAAGCG
1 ACCTATTACATTATATAAGCG
2879093 ACCTATTACATTATATAAGCG
1 ACCTATTACATTATATAAGCG
2879114 TTGCCTAATA
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:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
ACCTATTACATTATATAAGCG
Found at i:2880297 original size:139 final size:140
Alignment explanation
Indices: 2880067--2880327 Score: 366
Period size: 139 Copynumber: 1.9 Consensus size: 140
2880057 GAACATAGGG
*
2880067 ATTAAACCTAAAACACAAGCTCTAATTATTAATCCTAATCAATTTTAACAAATTACGAAATCAAA
1 ATTAAACCTAAAACACAAGCTCTAATTATTAATCCTAACCAATTTTAACAAATTACGAAATCAAA
*
2880132 TAACTAAAATGGAACCTCATACATTAATACGAG-ACCAAATAAAAAATTCACCTAAATTTAGGGA
66 TAACTAAAATGGAACCTCAGACATTAATACGAGAACCAAATAAAAAATTCACCTAAATTTAGGGA
2880196 CTAAAGTGAA
131 CTAAAGTGAA
* * * * *
2880206 ATTAAACCTAAAATGA-AATCTCTAA-TATTAATCCTAACCAATTTTAACCAATTATTGGAATCA
1 ATTAAACCTAAAA-CACAAGCTCTAATTATTAATCCTAACCAATTTTAACAAATTA-CGAAATCA
* * ** * *
2880269 AATAATTAAAATGGAACCTCGGGTATTAATATGAGAACCAAATCAAAAATTCACCTAAA
64 AATAACTAAAATGGAACCTCAGACATTAATACGAGAACCAAATAAAAAATTCACCTAAA
2880328 CTAAAAAAGT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
138 27 0.25
139 56 0.53
140 23 0.22
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (140 bp):
ATTAAACCTAAAACACAAGCTCTAATTATTAATCCTAACCAATTTTAACAAATTACGAAATCAAA
TAACTAAAATGGAACCTCAGACATTAATACGAGAACCAAATAAAAAATTCACCTAAATTTAGGGA
CTAAAGTGAA
Found at i:2881313 original size:21 final size:21
Alignment explanation
Indices: 2881289--2881334 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
2881279 CATGTTGGAC
2881289 AAAACAAAATCCTAAATTATG
1 AAAACAAAATCCTAAATTATG
2881310 AAAACAAAATCCTAAATTATG
1 AAAACAAAATCCTAAATTATG
2881331 AAAA
1 AAAA
2881335 ATATGTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (21 bp):
AAAACAAAATCCTAAATTATG
Found at i:2881909 original size:21 final size:20
Alignment explanation
Indices: 2881861--2881899 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2881851 TCAACAACGA
* *
2881861 AGGGATCGATCCTTTTTGAG
1 AGGGATCAATCCTTTTTCAG
2881881 AGGGATCAATCCTTTTTCA
1 AGGGATCAATCCTTTTTCA
2881900 CGGGGTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
AGGGATCAATCCTTTTTCAG
Found at i:2895235 original size:15 final size:16
Alignment explanation
Indices: 2895217--2895246 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2895207 AATAGAAATC
2895217 AAAGAGAAA-AAAAGA
1 AAAGAGAAAGAAAAGA
2895232 AAAGAGAAAGAAAAG
1 AAAGAGAAAGAAAAG
2895247 TGCTCAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAGAAAGAAAAGA
Found at i:2897727 original size:2 final size:2
Alignment explanation
Indices: 2897720--2897761 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2897710 TATGCAGTTA
2897720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2897762 GCAATTGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2899956 original size:275 final size:275
Alignment explanation
Indices: 2899465--2900012 Score: 997
Period size: 275 Copynumber: 2.0 Consensus size: 275
2899455 GAAGTGCTAA
*
2899465 ATCAATATGACACATTGAGTTCGTTCCCACCATTAGTACTAGGTATCCTTTAATACTAATCCGCA
1 ATCAATATGACACATTGAGTTCGTTCCCACCATTAATACTAGGTATCCTTTAATACTAATCCGCA
* *
2899530 CTAGGTATCCTTTAGTATGACCTCGAATATGAAAGATAAGGTCGTGCCCACTATATGCACTAAGT
66 CTACGTATCCTTTAGTATGACCTCGAATATGAAACATAAGGTCGTGCCCACTATATGCACTAAGT
2899595 ATCCTTTTGTACTATACTAGGTATCCTTTAGTGCTAAACCAATATGCAACTGCTACTAGACTCTA
131 ATCCTTTTGTACTATACTAGGTATCCTTTAGTGCTAAACCAATATGCAACTGCTACTAGACTCTA
2899660 TGGCATGGCAACTATAACAATGTCCGTCAATGACATACTTTGGCATATAGTTTACATTTATTCCA
196 TGGCATGGCAACTATAACAATGTCCGTCAATGACATACTTTGGCATATAGTTTACATTTATTCCA
2899725 ACCATGGAAATGTAT
261 ACCATGGAAATGTAT
* * *
2899740 ATCAATATGACACATTGAGTTCGTTCCCACTATTAATACTAGGTATCCTTTAATACTAATCTGTA
1 ATCAATATGACACATTGAGTTCGTTCCCACCATTAATACTAGGTATCCTTTAATACTAATCCGCA
* *
2899805 CTACGTATCCTTTAGTATGCCCTTGAATATGAAACATAAGGTCGTGCCCACTATATGCACTAAGT
66 CTACGTATCCTTTAGTATGACCTCGAATATGAAACATAAGGTCGTGCCCACTATATGCACTAAGT
*
2899870 ATCCTTTTGTACTATACTAGGTATCCTTTAGTGCTAAACCGATATGCAACTGCTACTAGACTCTA
131 ATCCTTTTGTACTATACTAGGTATCCTTTAGTGCTAAACCAATATGCAACTGCTACTAGACTCTA
*
2899935 TGGCATGGCAAGTATAACAATGTCCGTCAATGACATACTTTGGCATATAGTTTACATTTATTCCA
196 TGGCATGGCAACTATAACAATGTCCGTCAATGACATACTTTGGCATATAGTTTACATTTATTCCA
*
2900000 ACCATGGCAATGT
261 ACCATGGAAATGT
2900013 CCGTCAATGA
Statistics
Matches: 262, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
275 262 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (275 bp):
ATCAATATGACACATTGAGTTCGTTCCCACCATTAATACTAGGTATCCTTTAATACTAATCCGCA
CTACGTATCCTTTAGTATGACCTCGAATATGAAACATAAGGTCGTGCCCACTATATGCACTAAGT
ATCCTTTTGTACTATACTAGGTATCCTTTAGTGCTAAACCAATATGCAACTGCTACTAGACTCTA
TGGCATGGCAACTATAACAATGTCCGTCAATGACATACTTTGGCATATAGTTTACATTTATTCCA
ACCATGGAAATGTAT
Found at i:2907529 original size:75 final size:76
Alignment explanation
Indices: 2907400--2907553 Score: 256
Period size: 75 Copynumber: 2.0 Consensus size: 76
2907390 TAATATAACA
* *
2907400 AAATGGTAATTCACAAATTCATTATGAATACCATGGATGCACATAAAGTACCGAAAGTACACAAA
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACAAAGTACCGAAAGTACACAAA
2907465 GTACTGATACG
66 GTACTGATACG
* * *
2907476 AAATGGTAATTCA-TAACTCATTATGAATACCATGGATGCACACATAGTGCCGAAAGTACACAAA
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACAAAGTACCGAAAGTACACAAA
2907540 GTACTGATACG
66 GTACTGATACG
2907551 AAA
1 AAA
2907554 ATGCAACATA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
75 60 0.82
76 13 0.18
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (76 bp):
AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACAAAGTACCGAAAGTACACAAA
GTACTGATACG
Found at i:2921063 original size:11 final size:11
Alignment explanation
Indices: 2921050--2921103 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
2921040 AATTTTGGCT
*
2921050 TTTTTTTTTTT
1 TTTTTTTTTTG
2921061 TTTTTTTTTTG
1 TTTTTTTTTTG
**
2921072 CCCTTTTTTTTG
1 -TTTTTTTTTTG
*
2921084 TCTTTTTTTTG
1 TTTTTTTTTTG
2921095 TTTTTTTTT
1 TTTTTTTTT
2921104 GAAAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:2924626 original size:17 final size:17
Alignment explanation
Indices: 2924606--2924664 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2924596 ATTAGGGAAA
2924606 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
2924623 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
2924639 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
2924656 TAGTTCATT
1 TAGTTCATT
2924665 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:2924678 original size:18 final size:18
Alignment explanation
Indices: 2924655--2924700 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2924645 ATTCATGCAT
2924655 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
2924673 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
2924691 TTATTTCATT
1 TTAGTTCATT
2924701 AATCAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:2929833 original size:137 final size:137
Alignment explanation
Indices: 2929635--2929942 Score: 528
Period size: 137 Copynumber: 2.3 Consensus size: 137
2929625 GCAAGCATGC
* * *
2929635 AAATAAGCTTATGATCTTATGGAAT-AATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGATTACAAGCTTAT
2929699 GGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTAT
66 GGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTAT
2929764 ATTGGTA
131 ATTGGTA
* *
2929771 AAATAAGCTTACGAGATTATGGAATAAATGGTAAGTATATTGGTAAAATAAGATTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGATTACAAGCTTAT
**
2929836 GGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGGATTAAATGGTAAGTAT
66 GGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTAT
*
2929901 TTTGGTA
131 ATTGGTA
*
2929908 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
2929943 AGATTTTATC
Statistics
Matches: 161, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
136 22 0.14
137 139 0.86
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33
Consensus pattern (137 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGATTACAAGCTTAT
GGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTAT
ATTGGTA
Found at i:2929837 original size:91 final size:92
Alignment explanation
Indices: 2929635--2929942 Score: 498
Period size: 91 Copynumber: 3.4 Consensus size: 92
2929625 GCAAGCATGC
* * * *
2929635 AAATAAGCTTATGATCTTAT-GGAAT-AATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
2929698 TGGGATTAAATGGTAAGTATATTGGTA
66 TGGGATTAAATGGTAAGTATATTGGTA
* *
2929725 AAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGATTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
2929790 T-GGAATAAATGGTAAGTATATTGGTA
66 TGGGATTAAATGGTAAGTATATTGGTA
* *
2929816 AAATAAGATTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
2929881 TGGGATTAAATGGTAAGTATTTTGGTA
66 TGGGATTAAATGGTAAGTATATTGGTA
2929908 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
2929943 AGATTTTATC
Statistics
Matches: 201, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
90 17 0.08
91 101 0.50
92 83 0.41
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33
Consensus pattern (92 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGGGATTAAATGGTAAGTATATTGGTA
Found at i:2929949 original size:46 final size:46
Alignment explanation
Indices: 2929635--2929942 Score: 498
Period size: 46 Copynumber: 6.8 Consensus size: 46
2929625 GCAAGCATGC
* * *
2929635 AAATAAGCTTATGATCTTAT-GGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
*
2929679 AAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
*
2929725 AAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
* *
2929771 AAATAAGCTTACGAGATTAT-GGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
*
2929816 AAATAAGATTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
* *
2929862 AAATAAGCTTATGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
2929908 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
2929943 AGATTTTATC
Statistics
Matches: 247, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
44 17 0.07
45 57 0.23
46 173 0.70
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
Found at i:2934348 original size:17 final size:17
Alignment explanation
Indices: 2934326--2934373 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
2934316 TAAATGATGA
*
2934326 AAAAATCAATAAAAGAG
1 AAAAATAAATAAAAGAG
* *
2934343 AAAAATAAAGAAAAAAG
1 AAAAATAAATAAAAGAG
2934360 -AAAATAAATAAAAG
1 AAAAATAAATAAAAG
2934374 GGGGTTCAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAATAAATAAAAGAG
Found at i:2956054 original size:41 final size:42
Alignment explanation
Indices: 2955988--2956071 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
2955978 TAAAGCAGAA
2955988 AATAATTGTTTAGGCAAAACAAAGATTAACACCAAGTAAGAC
1 AATAATTGTTTAGGCAAAACAAAGATTAACACCAAGTAAGAC
2956030 AATAATTGTTTA-GCAAAACAAAGATTAACACCAAGTAAGAC
1 AATAATTGTTTAGGCAAAACAAAGATTAACACCAAGTAAGAC
2956071 A
1 A
2956072 GTTCATGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 30 0.71
42 12 0.29
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.21
Consensus pattern (42 bp):
AATAATTGTTTAGGCAAAACAAAGATTAACACCAAGTAAGAC
Found at i:2961832 original size:3 final size:3
Alignment explanation
Indices: 2961824--2961857 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2961814 GGAGTCTGCC
2961824 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2961858 ATTGTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2964170 original size:131 final size:130
Alignment explanation
Indices: 2963949--2964183 Score: 344
Period size: 131 Copynumber: 1.8 Consensus size: 130
2963939 AATATTGAAA
* * ** * * *
2963949 ATAGTTATATCTTTTCATTTTGATTGAGCAATAACTGACTGCTTTAAGGTATAAGTGGTCATTTA
1 ATAGTGATATCTCTTCATTACGATTGAGCAATAAATGACTGCTTTAAGGCATAAGAGGTCATTTA
*
2964014 TTCTCAATTGGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGAATTTTAAGACGAG
66 TTCTCAATTGGAAATAATTAGATATTATAGTTTTCTCTCAAATCAATATTGAATTTTAAGACGAG
* *
2964079 ATAGTGATATCTCTTCATTACGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTT
1 ATAGTGATATCTCTTCATTACGATT-GAGCAATAAATGACTGCTTTAAGGCATAAGAGGTCATTT
* * *
2964144 ATTCTCGATTGGAAATAATTATATATTATATTTTTCTCTC
65 ATTCTCAATTGGAAATAATTAGATATTATAGTTTTCTCTC
2964184 TTAAAATCCA
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
130 21 0.23
131 70 0.77
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (130 bp):
ATAGTGATATCTCTTCATTACGATTGAGCAATAAATGACTGCTTTAAGGCATAAGAGGTCATTTA
TTCTCAATTGGAAATAATTAGATATTATAGTTTTCTCTCAAATCAATATTGAATTTTAAGACGAG
Found at i:2978053 original size:21 final size:20
Alignment explanation
Indices: 2978028--2978072 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2978018 TGGAAATTGA
2978028 TGAAAATTGATG-TAGAATGCT
1 TGAAAA-TGATGTTAGAAT-CT
*
2978049 TGAAAATGTTGTTAGAATCT
1 TGAAAATGATGTTAGAATCT
2978069 TGAA
1 TGAA
2978073 TTTGAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (20 bp):
TGAAAATGATGTTAGAATCT
Found at i:2979743 original size:14 final size:14
Alignment explanation
Indices: 2979724--2979751 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2979714 AATTGTGGTT
2979724 TTATTGATTTTAAA
1 TTATTGATTTTAAA
2979738 TTATTGATTTTAAA
1 TTATTGATTTTAAA
2979752 GGAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTATTGATTTTAAA
Found at i:2980519 original size:19 final size:20
Alignment explanation
Indices: 2980495--2980541 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2980485 CTAAATCTTT
*
2980495 TTTTCAAAATT-TTATTTTG
1 TTTTCAAAATTCTAATTTTG
2980514 TTTTC-AAATTCTAATTTTG
1 TTTTCAAAATTCTAATTTTG
*
2980533 TTATCAAAA
1 TTTTCAAAA
2980542 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTCAAAATTCTAATTTTG
Found at i:2990637 original size:19 final size:19
Alignment explanation
Indices: 2990613--2990655 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2990603 AGAGCATTTA
*
2990613 TTTCATTAAAATTATGTAT
1 TTTCATAAAAATTATGTAT
*
2990632 TTTCATAAAAATTATGTGT
1 TTTCATAAAAATTATGTAT
2990651 TTTCA
1 TTTCA
2990656 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTCATAAAAATTATGTAT
Found at i:2991087 original size:35 final size:35
Alignment explanation
Indices: 2990998--2991099 Score: 105
Period size: 35 Copynumber: 2.9 Consensus size: 35
2990988 ACTATCTGTT
* *
2990998 CATCACCATTTTCACGCCTATAACATCACCATCTTC
1 CATCAACA-TTTCAAGCCTATAACATCACCATCTTC
* **
2991034 CATCACCATTAAAAGCCTATAACATCACCATCTTC
1 CATCAACATTTCAAGCCTATAACATCACCATCTTC
* * * * *
2991069 TATTAATATTTCATGCCTATACCATCACCAT
1 CATCAACATTTCAAGCCTATAACATCACCAT
2991100 TCCTTAACCA
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
35 47 0.85
36 8 0.15
ACGTcount: A:0.32, C:0.33, G:0.03, T:0.31
Consensus pattern (35 bp):
CATCAACATTTCAAGCCTATAACATCACCATCTTC
Found at i:2991484 original size:13 final size:13
Alignment explanation
Indices: 2991466--2991536 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
2991456 GTGCTACAAC
2991466 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
*
2991479 AAGAAGAAAAATA
1 AAGAAGAAAAAGA
2991492 AA-AGAGAAAAAAGA
1 AAGA-AG-AAAAAGA
2991506 AAGAAGAGAAACA-A
1 AAGAAGA-AAA-AGA
2991520 AAG-AGAAAATAGA
1 AAGAAGAAAA-AGA
2991533 AAGA
1 AAGA
2991537 CTCCTACAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
12 5 0.10
13 24 0.50
14 17 0.35
15 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:2991487 original size:7 final size:6
Alignment explanation
Indices: 2991469--2991534 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 6
2991459 CTACAACAAG
* * *
2991469 AAGAAA AAGAAA GAAGAAA AATAAA AGAGAAAA AAGAAA GAAGAGA AACAAA
1 AAGAAA AAGAAA -AAGAAA AAGAAA A-AG-AAA AAGAAA -AAGAAA AAGAAA
2991521 AGAGAAA ATAGAAA
1 A-AGAAA A-AGAAA
2991535 GACTCCTACA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
6 20 0.42
7 24 0.50
8 4 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:2991496 original size:27 final size:26
Alignment explanation
Indices: 2991461--2991536 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
2991451 TCAAAGTGCT
2991461 ACAACAAGAAGAAAAAGAAAGAAGAAAA
1 ACAA-AAG-AGAAAAAGAAAGAAGAAAA
* *
2991489 ATAAAAGAGAAAAAAGAAAGAAGAGAA
1 ACAAAAGAG-AAAAAGAAAGAAGAAAA
2991516 ACAAAAGAGAAAATAGAAAGA
1 ACAAAAGAGAAAA-AGAAAGA
2991537 CTCCTACAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.14
27 34 0.79
28 3 0.07
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.03
Consensus pattern (26 bp):
ACAAAAGAGAAAAAGAAAGAAGAAAA
Found at i:2992953 original size:24 final size:24
Alignment explanation
Indices: 2992926--2992988 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2992916 GTCCTTAGAT
*
2992926 GTTCCAACAGTTATGCCACTTGAA
1 GTTCCAAAAGTTATGCCACTTGAA
* * * *
2992950 GTTCAAAAAGATGTGTCACTTGAA
1 GTTCCAAAAGTTATGCCACTTGAA
*
2992974 GTGCCAAAAGTTATG
1 GTTCCAAAAGTTATG
2992989 ATCATTGAAG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (24 bp):
GTTCCAAAAGTTATGCCACTTGAA
Found at i:2994793 original size:20 final size:19
Alignment explanation
Indices: 2994758--2994799 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2994748 AGATTTTATC
*
2994758 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
2994777 TTCATTAAAAATCATGTGTT
1 TTCATT-AAAATCATGTATT
2994797 TTC
1 TTC
2994800 GAAGGGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:2995156 original size:13 final size:13
Alignment explanation
Indices: 2995133--2995166 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2995123 ATAAGATACT
2995133 ATCTGTTCATCACC
1 ATCT-TTCATCACC
2995147 ATCTTTCATCACC
1 ATCTTTCATCACC
2995160 AT-TTTCA
1 ATCTTTCA
2995167 CGCCTATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 11 0.55
14 4 0.20
ACGTcount: A:0.24, C:0.32, G:0.03, T:0.41
Consensus pattern (13 bp):
ATCTTTCATCACC
Found at i:2995214 original size:35 final size:36
Alignment explanation
Indices: 2995140--2995254 Score: 135
Period size: 35 Copynumber: 3.2 Consensus size: 36
2995130 ACTATCTGTT
* **
2995140 CATCACCATCTTTCATCACCATTTTCACGCCTATAA
1 CATCACCATCTTCCATCACCATTTAAACGCCTATAA
* *
2995176 CATCACCATCTTCCATCATCA-TTAAATGCCTATAA
1 CATCACCATCTTCCATCACCATTTAAACGCCTATAA
* * * *
2995211 CATCACCATCTTCTATTACCATTT-CACGCCTATAT
1 CATCACCATCTTCCATCACCATTTAAACGCCTATAA
2995246 CATCACCAT
1 CATCACCAT
2995255 TCCTTAACCA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
35 46 0.69
36 21 0.31
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.33
Consensus pattern (36 bp):
CATCACCATCTTCCATCACCATTTAAACGCCTATAA
Found at i:3004692 original size:17 final size:17
Alignment explanation
Indices: 3004672--3004709 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3004662 GGTCAAAGGA
*
3004672 GGTCAACGGTCGGGTCG
1 GGTCAACGGCCGGGTCG
*
3004689 GGTCAATGGCCGGGTCG
1 GGTCAACGGCCGGGTCG
3004706 GGTC
1 GGTC
3004710 GGGTCAGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGCCGGGTCG
Found at i:3004752 original size:9 final size:9
Alignment explanation
Indices: 3004711--3004775 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
3004701 GGTCGGGTCG
*
3004711 GGTCAGACC
1 GGTCAAACC
*
3004720 GGTCAGACC
1 GGTCAAACC
*
3004729 GGTTCGAA-C
1 GG-TCAAACC
3004738 GGTCAAACC
1 GGTCAAACC
3004747 GGTCAAAACC
1 GGTC-AAACC
*
3004757 GGTTCAAAACT
1 GG-TC-AAACC
3004768 GGTCAAAC
1 GGTCAAAC
3004776 TGGTTTTCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.08
9 23 0.48
10 12 0.25
11 9 0.19
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3004779 original size:9 final size:10
Alignment explanation
Indices: 3004737--3004774 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
3004727 CCGGTTCGAA
3004737 CGGTC-AAAC
1 CGGTCAAAAC
3004746 CGGTCAAAAC
1 CGGTCAAAAC
3004756 CGGTTCAAAAC
1 CGG-TCAAAAC
*
3004767 TGGTCAAA
1 CGGTCAAA
3004775 CTGGTTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 5 0.19
10 12 0.46
11 9 0.35
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (10 bp):
CGGTCAAAAC
Found at i:3011440 original size:19 final size:19
Alignment explanation
Indices: 3011413--3011465 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3011403 CGGTTTTGAT
*
3011413 CGGTTTGACCAGT-TCAAAC
1 CGGTTTGACCGGTCT-AAAC
*
3011432 CGGTCTGACCGGTCTAAAC
1 CGGTTTGACCGGTCTAAAC
3011451 CGGTTTGACCGGTCT
1 CGGTTTGACCGGTCT
3011466 GACCCGACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 29 0.97
20 1 0.03
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (19 bp):
CGGTTTGACCGGTCTAAAC
Found at i:3011444 original size:9 final size:9
Alignment explanation
Indices: 3011430--3011469 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3011420 ACCAGTTCAA
3011430 ACCGGTCTG
1 ACCGGTCTG
*
3011439 ACCGGTCTAA
1 ACCGGTCT-G
*
3011449 ACCGGTTTG
1 ACCGGTCTG
3011458 ACCGGTCTG
1 ACCGGTCTG
3011467 ACC
1 ACC
3011470 CGACCCGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.23
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:3015887 original size:18 final size:17
Alignment explanation
Indices: 3015861--3015894 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3015851 TGCCTAAGGT
3015861 AAAAATTAAGTTGAATTG
1 AAAAATTAAGTT-AATTG
*
3015879 AAAATTTAAGTTAATT
1 AAAAATTAAGTTAATT
3015895 AAATTGAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAATTAAGTTAATTG
Found at i:3029675 original size:40 final size:40
Alignment explanation
Indices: 3029596--3029675 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
3029586 ATAAGAGTCA
* * *
3029596 AATATTGCACAATAGTGATGAGGTCGAGCTTTACTCACCT
1 AATATTGCACAATAGTCATAAGGTCGAGCTTTACCCACCT
* * * *
3029636 AATATTGCACAGTAGTCCTAAGGTCGGGCTTTGCCCACCT
1 AATATTGCACAATAGTCATAAGGTCGAGCTTTACCCACCT
3029676 GACTTTTACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (40 bp):
AATATTGCACAATAGTCATAAGGTCGAGCTTTACCCACCT
Found at i:3029950 original size:24 final size:24
Alignment explanation
Indices: 3029918--3029966 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3029908 AGTCTTCCTG
*
3029918 ATGATGTATAAAACACCTATGTAC
1 ATGATGTATAAAACACATATGTAC
*
3029942 ATGATGTATAAAACATATATGTAC
1 ATGATGTATAAAACACATATGTAC
3029966 A
1 A
3029967 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (24 bp):
ATGATGTATAAAACACATATGTAC
Found at i:3031180 original size:11 final size:11
Alignment explanation
Indices: 3031164--3031188 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3031154 TTTCAAGCTA
3031164 AATTTACCTTT
1 AATTTACCTTT
3031175 AATTTACCTTT
1 AATTTACCTTT
3031186 AAT
1 AAT
3031189 GAATATTAAA
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTACCTTT
Found at i:3031667 original size:29 final size:29
Alignment explanation
Indices: 3031586--3031672 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
3031576 GGCCAAATTG
* * *
3031586 TAACTTTAAAATTAATATTTTTGTCACTA
1 TAACTTTAAAATTTATAATTTGGTCACTA
* *
3031615 TAATTTTTTAAAGTTTA-AACTTTGGTCACT-
1 TAA--CTTTAAAATTTATAA-TTTGGTCACTA
3031645 TAACTTTAAAAATTTATAATTTGGTCAC
1 TAACTTT-AAAATTTATAATTTGGTCAC
3031673 AAACTAAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 3 0.07
29 19 0.41
30 6 0.13
31 18 0.39
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (29 bp):
TAACTTTAAAATTTATAATTTGGTCACTA
Found at i:3032236 original size:10 final size:10
Alignment explanation
Indices: 3032223--3032255 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3032213 AAAAAAAACA
3032223 AAAAAAGGCG
1 AAAAAAGGCG
*
3032233 AAAAAAGGTG
1 AAAAAAGGCG
3032243 AAAAAAGGC-
1 AAAAAAGGCG
3032252 AAAA
1 AAAA
3032256 CAAAAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.67, C:0.06, G:0.24, T:0.03
Consensus pattern (10 bp):
AAAAAAGGCG
Found at i:3036827 original size:20 final size:20
Alignment explanation
Indices: 3036797--3036842 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
3036787 GCTATTTTTT
*
3036797 CAAACAAAAAACAAAAAAAGC
1 CAAA-AAAAAAAAAAAAAAGC
3036818 CAAAAAAAAAAAAAAAAAGC
1 CAAAAAAAAAAAAAAAAAGC
3036838 CAAAA
1 CAAAA
3036843 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.80, C:0.15, G:0.04, T:0.00
Consensus pattern (20 bp):
CAAAAAAAAAAAAAAAAAGC
Found at i:3046460 original size:19 final size:19
Alignment explanation
Indices: 3046436--3046473 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3046426 ATAAGATTAG
3046436 AATAAAAAAAACATAAGAT
1 AATAAAAAAAACATAAGAT
* *
3046455 AATAAAGAAATCATAAGAT
1 AATAAAAAAAACATAAGAT
3046474 CTCCTTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (19 bp):
AATAAAAAAAACATAAGAT
Found at i:3052007 original size:90 final size:90
Alignment explanation
Indices: 3051887--3052064 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
3051877 TAATCCCGAA
* * * * *
3051887 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
3051952 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
3051977 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
3052042 TAGGGTAACTTGGATATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
3052065 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:3053324 original size:24 final size:24
Alignment explanation
Indices: 3053292--3053339 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3053282 GTCTTCTTGT
3053292 TGATGTATAAAACATCTACGTACA
1 TGATGTATAAAACATCTACGTACA
*
3053316 TGATGTATAAAACATCTATGTACA
1 TGATGTATAAAACATCTACGTACA
3053340 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (24 bp):
TGATGTATAAAACATCTACGTACA
Found at i:3056818 original size:10 final size:10
Alignment explanation
Indices: 3056803--3056827 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3056793 TAGATTTTAA
3056803 GAGTTTAATT
1 GAGTTTAATT
3056813 GAGTTTAATT
1 GAGTTTAATT
3056823 GAGTT
1 GAGTT
3056828 GATTCTTAAG
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:0.24, T:0.48
Consensus pattern (10 bp):
GAGTTTAATT
Found at i:3074815 original size:23 final size:23
Alignment explanation
Indices: 3074780--3074824 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3074770 AATGGAGGAA
*
3074780 TGGTCACTTTGATGTTGCTGAAG
1 TGGTCACTTTGATGTTGATGAAG
*
3074803 TGGTCA-TTCTGATTTTGATGAA
1 TGGTCACTT-TGATGTTGATGAA
3074825 CATCTCTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42
Consensus pattern (23 bp):
TGGTCACTTTGATGTTGATGAAG
Found at i:3093070 original size:33 final size:33
Alignment explanation
Indices: 3093033--3093097 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
3093023 TTATTTAAGG
*
3093033 CATAACATATATACACTACAAACGTTAACATGT
1 CATAACATATATACACTACAAACGATAACATGT
**
3093066 CATAACATATATACACTATTAACGATAACATG
1 CATAACATATATACACTACAAACGATAACATG
3093098 CTTTCATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (33 bp):
CATAACATATATACACTACAAACGATAACATGT
Found at i:3118647 original size:19 final size:19
Alignment explanation
Indices: 3118625--3118680 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3118615 CATTTCAAAT
3118625 TCATAACTCTTTTTCATAC
1 TCATAACTCTTTTTCATAC
* *
3118644 TCATAACTCATTTTT-AGAT
1 TCATAACTC-TTTTTCATAC
* *
3118663 TCAGAACTCATTTTCATA
1 TCATAACTCTTTTTCATA
3118681 TTAATAGTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.13
19 21 0.70
20 5 0.17
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATAACTCTTTTTCATAC
Found at i:3118798 original size:34 final size:34
Alignment explanation
Indices: 3118741--3118819 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
3118731 GAGTGTGCGC
* *
3118741 AATAAGCACTCTAGGTGCTATCATCAAAAACATA
1 AATATGCACTCTAGGTGCAATCATCAAAAACATA
* *
3118775 AATATGCATTCTAGGTGCAATCATCAAATACATA
1 AATATGCACTCTAGGTGCAATCATCAAAAACATA
3118809 AATATGCACTC
1 AATATGCACTC
3118820 CAGTGGGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (34 bp):
AATATGCACTCTAGGTGCAATCATCAAAAACATA
Found at i:3119143 original size:12 final size:12
Alignment explanation
Indices: 3119104--3119145 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3119094 AATTTCATAC
3119104 CAAAAATCATT-
1 CAAAAATCATTA
* *
3119115 CAATAACCATTA
1 CAAAAATCATTA
3119127 CAAAAATCATTA
1 CAAAAATCATTA
*
3119139 TAAAAAT
1 CAAAAAT
3119146 AGTTCTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (12 bp):
CAAAAATCATTA
Found at i:3124878 original size:2 final size:2
Alignment explanation
Indices: 3124871--3124913 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3124861 TCATTTAACT
3124871 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
3124913 T
1 T
3124914 TCCCATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3125857 original size:34 final size:34
Alignment explanation
Indices: 3125780--3125862 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
3125770 CAATAAGCAA
* * *
3125780 TCCAGGTTCATTCATCATAGACATAAATATACAC
1 TCCAGGTGCATTCATCAGAGACAAAAATATACAC
* * *
3125814 TCCAAGTGCATTCATCAGATACAAAAATATGCAC
1 TCCAGGTGCATTCATCAGAGACAAAAATATACAC
* *
3125848 TCTAGGTGCAATCAT
1 TCCAGGTGCATTCAT
3125863 ATAATGTACA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (34 bp):
TCCAGGTGCATTCATCAGAGACAAAAATATACAC
Found at i:3128803 original size:28 final size:29
Alignment explanation
Indices: 3128771--3128839 Score: 122
Period size: 28 Copynumber: 2.4 Consensus size: 29
3128761 CCTAAACTTG
3128771 AACCCGACCCGAATATCACACTT-AAAAA
1 AACCCGACCCGAATATCACACTTAAAAAA
3128799 AACCCGACCCGAATATCACACTTAAAAAA
1 AACCCGACCCGAATATCACACTTAAAAAA
*
3128828 AACTCGACCCGA
1 AACCCGACCCGA
3128840 CCACGATTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 23 0.59
29 16 0.41
ACGTcount: A:0.45, C:0.33, G:0.09, T:0.13
Consensus pattern (29 bp):
AACCCGACCCGAATATCACACTTAAAAAA
Found at i:3128884 original size:31 final size:30
Alignment explanation
Indices: 3128850--3128907 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3128840 CCACGATTGT
** *
3128850 TTTTTAAAAAAATTCGACCCGATCCTGAAA
1 TTTTTAAAAAAACCCGACCCGACCCTGAAA
3128880 TTTTTAAAAAAACCCGACCCGACCCTGA
1 TTTTTAAAAAAACCCGACCCGACCCTGA
3128908 CTCGAATATC
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:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (30 bp):
TTTTTAAAAAAACCCGACCCGACCCTGAAA
Found at i:3128962 original size:48 final size:49
Alignment explanation
Indices: 3128891--3128993 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 49
3128881 TTTTAAAAAA
* * *
3128891 ACCCGACCCGACCCTGACTCGAATATCACACTTA-AAAAAACCGACCCT
1 ACCCGACCCGACCCTGACCCGAATATCAAACTTAGAAAAAACCGACCCG
* *
3128939 ACCCGACCTGAACCC-GACCCGAATATCAAACTTAGAAAAACCCGACCCG
1 ACCCGACCCG-ACCCTGACCCGAATATCAAACTTAGAAAAAACCGACCCG
3128988 ACCCGA
1 ACCCGA
3128994 ACTCGAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
48 26 0.54
49 22 0.46
ACGTcount: A:0.36, C:0.40, G:0.13, T:0.12
Consensus pattern (49 bp):
ACCCGACCCGACCCTGACCCGAATATCAAACTTAGAAAAAACCGACCCG
Found at i:3129064 original size:33 final size:32
Alignment explanation
Indices: 3128999--3129065 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
3128989 CCCGAACTCG
** * *
3128999 AATTTTTTTAAAAAAATCAGACCCGATCCCAA
1 AATTTTTAAAAAAAAATCAGACCCAATACCAA
*
3129031 AATTTTTAAAAAAAAATCTGACCCAAATACCAA
1 AATTTTTAAAAAAAAATCAGACCC-AATACCAA
3129064 AA
1 AA
3129066 GATTGATGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.25
Consensus pattern (32 bp):
AATTTTTAAAAAAAAATCAGACCCAATACCAA
Found at i:3142596 original size:31 final size:31
Alignment explanation
Indices: 3142550--3142608 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3142540 AAAAATTATG
* *
3142550 TTATTGTTTTATTAAGTTTTGGTCACTTACA
1 TTATCGTTTTATTAAGTTTTGATCACTTACA
*
3142581 TTATCGTTTTGTTAAGTTTTGATCACTT
1 TTATCGTTTTATTAAGTTTTGATCACTT
3142609 GGACATTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.56
Consensus pattern (31 bp):
TTATCGTTTTATTAAGTTTTGATCACTTACA
Found at i:3142995 original size:24 final size:24
Alignment explanation
Indices: 3142952--3142997 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3142942 GTTAAAATGA
**
3142952 TAAATGAACACAAATGAACGAAAG
1 TAAATGAACACAAACAAACGAAAG
*
3142976 TAAATGAACATAAACAAACGAA
1 TAAATGAACACAAACAAACGAA
3142998 CATAAATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (24 bp):
TAAATGAACACAAACAAACGAAAG
Found at i:3143003 original size:24 final size:23
Alignment explanation
Indices: 3142951--3143004 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
3142941 TGTTAAAATG
**
3142951 ATAAATGAACACAAATGAACGAA
1 ATAAATGAACACAAACAAACGAA
*
3142974 AGTAAATGAACATAAACAAACGAA
1 A-TAAATGAACACAAACAAACGAA
3142998 CATAAAT
1 -ATAAAT
3143005 CAATTGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.15
Consensus pattern (23 bp):
ATAAATGAACACAAACAAACGAA
Found at i:3143217 original size:10 final size:10
Alignment explanation
Indices: 3143202--3143234 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3143192 TAAATGAACA
3143202 AACATAAATG
1 AACATAAATG
*
3143212 AACAT-AACG
1 AACATAAATG
3143221 AACATAAATG
1 AACATAAATG
3143231 AACA
1 AACA
3143235 AACTAGCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.61, C:0.15, G:0.09, T:0.15
Consensus pattern (10 bp):
AACATAAATG
Found at i:3149608 original size:30 final size:31
Alignment explanation
Indices: 3149534--3149610 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
3149524 ATAAACGTCC
* * * * * *
3149534 AAGTTACCAAACCATAATAAAATAATAACGT
1 AAGTGACCAAAACTTAAGAAAACAATAACAT
3149565 AAGTGACCAAAACTTAAGAAAACAATAACAT
1 AAGTGACCAAAACTTAAGAAAACAATAACAT
*
3149596 AAGTG-GCAAAACTTA
1 AAGTGACCAAAACTTA
3149611 TATTTTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 9 0.23
31 30 0.77
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAAGAAAACAATAACAT
Found at i:3150543 original size:44 final size:45
Alignment explanation
Indices: 3150397--3150557 Score: 252
Period size: 45 Copynumber: 3.6 Consensus size: 45
3150387 TATAAAATTT
* * * *
3150397 CTTATCATTTATACGATAAGCTCATAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3150442 CTTACCGTTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
3150487 CTTACCATTTATTCCATAAGCTCGTAAGCTTA-TTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3150531 CTTACCAATTATTCCATAATCTCGTAA
1 CTTACCATTTATTCCATAAGCTCGTAA
3150558 CCAATTATTT
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 37 0.34
45 71 0.66
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3150560 original size:23 final size:23
Alignment explanation
Indices: 3150534--3150577 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3150524 CAATATACTT
*
3150534 ACCAATTATTCCATAATCTCGTA
1 ACCAATTATTCCATAAGCTCGTA
*
3150557 ACCAATTATTTCATAAGCTCG
1 ACCAATTATTCCATAAGCTCG
3150578 CAAGCTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (23 bp):
ACCAATTATTCCATAAGCTCGTA
Found at i:3150575 original size:67 final size:66
Alignment explanation
Indices: 3150490--3150623 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 66
3150480 CAATATACTT
* * * *
3150490 ACCATTTATTCCATAAGCTCGTAAGCTTATTTACCAATATACTTACCAATTATTCCATAATCTCG
1 ACCAATTATTCCATAAGCTCGCAAGCTTAGTTACCAATATACTTACC-ATTATTCCATAAGCTCG
3150555 TA
65 TA
* *
3150557 ACCAATTATTTCATAAGCTCGCAAGCTTAGTTACCAATATACTTGCCATTATTCCATAAGCTCGT
1 ACCAATTATTCCATAAGCTCGCAAGCTTAGTTACCAATATACTTACCATTATTCCATAAGCTCGT
3150622 A
66 A
3150623 A
1 A
3150624 GCTTATTTGC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 19 0.31
67 42 0.69
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (66 bp):
ACCAATTATTCCATAAGCTCGCAAGCTTAGTTACCAATATACTTACCATTATTCCATAAGCTCGT
A
Found at i:3154255 original size:14 final size:13
Alignment explanation
Indices: 3154235--3154269 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3154225 CTTCAAAACA
3154235 TTTTTAATTTAAT
1 TTTTTAATTTAAT
*
3154248 TATTTTAATTTTAT
1 T-TTTTAATTTAAT
3154262 TTTTTAAT
1 TTTTTAAT
3154270 AAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:3154563 original size:25 final size:27
Alignment explanation
Indices: 3154505--3154563 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
3154495 TATTATTAAA
* *
3154505 TTAATTTAAAAATATGTTATTTTTATT
1 TTAATTTAAAAATATGATATATTTATT
*
3154532 TTCATTTAAAAATAT-ATA-ATTTATT
1 TTAATTTAAAAATATGATATATTTATT
3154557 TTAATTT
1 TTAATTT
3154564 GTTAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 12 0.43
26 2 0.07
27 14 0.50
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTAATTTAAAAATATGATATATTTATT
Found at i:3155563 original size:17 final size:17
Alignment explanation
Indices: 3155538--3155577 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3155528 GTATGTTGTT
*
3155538 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
3155555 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
3155572 CATTTA
1 CATTTA
3155578 TGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:3159088 original size:7 final size:7
Alignment explanation
Indices: 3159076--3159128 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
3159066 CATAATCAGA
3159076 TTTAGGG
1 TTTAGGG
3159083 TTTAGGG
1 TTTAGGG
3159090 TTTAGGG
1 TTTAGGG
3159097 TTTAGGG
1 TTTAGGG
**
3159104 TTTATAG
1 TTTAGGG
* *
3159111 TTTATGA
1 TTTAGGG
3159118 TTTAGGG
1 TTTAGGG
3159125 TTTA
1 TTTA
3159129 TCACAAAGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:3159203 original size:14 final size:14
Alignment explanation
Indices: 3159181--3159233 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
3159171 GTAAGTATAA
*
3159181 TTTAGGGTTTATGG
1 TTTAGGGTTTATGT
* *
3159195 TTTATGGTTCATGT
1 TTTAGGGTTTATGT
*
3159209 TTTATGGTTTATGT
1 TTTAGGGTTTATGT
3159223 TTTAGGGTTTA
1 TTTAGGGTTTA
3159234 GAGTTTAGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.15, C:0.02, G:0.26, T:0.57
Consensus pattern (14 bp):
TTTAGGGTTTATGT
Found at i:3159234 original size:7 final size:7
Alignment explanation
Indices: 3159181--3159233 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
3159171 GTAAGTATAA
*
3159181 TTTAGGG
1 TTTATGG
3159188 TTTATGG
1 TTTATGG
3159195 TTTATGG
1 TTTATGG
* *
3159202 TTCATGT
1 TTTATGG
3159209 TTTATGG
1 TTTATGG
*
3159216 TTTATGT
1 TTTATGG
*
3159223 TTTAGGG
1 TTTATGG
3159230 TTTA
1 TTTA
3159234 GAGTTTAGGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.15, C:0.02, G:0.26, T:0.57
Consensus pattern (7 bp):
TTTATGG
Found at i:3159240 original size:21 final size:21
Alignment explanation
Indices: 3159181--3159233 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3159171 GTAAGTATAA
3159181 TTTAGGGTTTATGGTTTATGG
1 TTTAGGGTTTATGGTTTATGG
* * * *
3159202 TTCATGTTTTATGGTTTATGT
1 TTTAGGGTTTATGGTTTATGG
3159223 TTTAGGGTTTA
1 TTTAGGGTTTA
3159234 GAGTTTAGGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.02, G:0.26, T:0.57
Consensus pattern (21 bp):
TTTAGGGTTTATGGTTTATGG
Found at i:3159310 original size:11 final size:11
Alignment explanation
Indices: 3159291--3159322 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3159281 GTATTATAGA
3159291 ATTTTTAATAT
1 ATTTTTAATAT
*
3159302 ATTTATAATAT
1 ATTTTTAATAT
3159313 ATTTTTAATA
1 ATTTTTAATA
3159323 ATGTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:3160463 original size:14 final size:14
Alignment explanation
Indices: 3160421--3160473 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
3160411 AATTTATTTA
*
3160421 TTTATTATTAAAAA
1 TTTATTATTAAAAT
* *
3160435 TTTATTTTTATAAT
1 TTTATTATTAAAAT
*
3160449 TTTATTAATAAAAT
1 TTTATTATTAAAAT
*
3160463 TATTAATATTA
1 T-TTATTATTA
3160474 GTACATTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
14 23 0.77
15 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTATTAAAAT
Found at i:3160518 original size:16 final size:16
Alignment explanation
Indices: 3160497--3160530 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3160487 AAATACAAAT
*
3160497 ATTATAAATTATATTA
1 ATTATAAATTAAATTA
*
3160513 ATTATATATTAAATTA
1 ATTATAAATTAAATTA
3160529 AT
1 AT
3160531 AGTATTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATAAATTAAATTA
Found at i:3160519 original size:21 final size:21
Alignment explanation
Indices: 3160495--3160546 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3160485 TGAAATACAA
*
3160495 ATATTATAAATT-ATATTAATT
1 ATATTATAAATTAATAGT-ATT
3160516 ATA-TATTAAATTAATAGTATT
1 ATATTA-TAAATTAATAGTATT
3160537 ATATTATAAA
1 ATATTATAAA
3160547 AGTATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 19 0.70
22 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTATAAATTAATAGTATT
Found at i:3161706 original size:11 final size:11
Alignment explanation
Indices: 3161690--3161752 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3161680 AAAATTACAT
3161690 TATTAAAAATA
1 TATTAAAAATA
3161701 TATTAAAAATA
1 TATTAAAAATA
* * ***
3161712 CACTATTGATA
1 TATTAAAAATA
3161723 -ATTATAAAAT-
1 TATTA-AAAATA
3161733 T-TTAAAAATA
1 TATTAAAAATA
3161743 TATTAAAAAT
1 TATTAAAAAT
3161753 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3161808 original size:7 final size:7
Alignment explanation
Indices: 3161795--3161855 Score: 79
Period size: 7 Copynumber: 8.7 Consensus size: 7
3161785 TGTTCTTGTA
3161795 ATAAACC
1 ATAAACC
*
3161802 CTAAACC
1 ATAAACC
3161809 ATAAATCC
1 ATAAA-CC
*
3161817 -TAAAAC
1 ATAAACC
3161823 ATAAACC
1 ATAAACC
3161830 ATAAACC
1 ATAAACC
3161837 ATAAACC
1 ATAAACC
3161844 ATAAACC
1 ATAAACC
*
3161851 CTAAA
1 ATAAA
3161856 ATGTAATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 1 0.02
7 44 0.94
8 2 0.04
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (7 bp):
ATAAACC
Found at i:3161927 original size:14 final size:13
Alignment explanation
Indices: 3161908--3161964 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
3161898 ATCTTTGCAA
3161908 TAAACCCTAAACTC
1 TAAACCCTAAA-TC
3161922 TAAACCCTAAATC
1 TAAACCCTAAATC
** *
3161935 ATAAACTATAAACCC
1 -TAAACCCTAAA-TC
3161950 TAAA-CCTAAATC
1 TAAACCCTAAATC
3161962 TAA
1 TAA
3161965 TTATGTGATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.11
13 6 0.17
14 24 0.69
15 1 0.03
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAACCCTAAATC
Found at i:3178598 original size:23 final size:25
Alignment explanation
Indices: 3178563--3178617 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
3178553 AAATCCAACA
*
3178563 AAGAAAATCAAAGCAC-TCAAAA-G
1 AAGAAAATCAAAGCACTTAAAAAGG
* *
3178586 AAGAAATTGAAAGCACTTAAAAAGG
1 AAGAAAATCAAAGCACTTAAAAAGG
3178611 AAGAAAA
1 AAGAAAA
3178618 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 14 0.54
24 5 0.19
25 7 0.27
ACGTcount: A:0.62, C:0.11, G:0.16, T:0.11
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTTAAAAAGG
Found at i:3182715 original size:21 final size:21
Alignment explanation
Indices: 3182676--3182715 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3182666 ATACATTCTT
* * *
3182676 ATTAGCTCATAGACTTTATAC
1 ATTAGCTCACAAACATTATAC
3182697 ATTAGCTCACAAACATTAT
1 ATTAGCTCACAAACATTAT
3182716 TAGATGATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACAAACATTATAC
Found at i:3183681 original size:44 final size:44
Alignment explanation
Indices: 3183568--3183717 Score: 228
Period size: 45 Copynumber: 3.4 Consensus size: 44
3183558 AAATTCTTAT
* **
3183568 CAATTTACTTACCATTTATCTTATAAGCTCGTAAGCTTATTTTA
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
*
3183612 CAAATTTACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 C-AATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
*
3183657 CAATATACTTACCATTTATCCCATAAGCTTGTAAGCTTATTTTA
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
*
3183701 CCAATATACTTTCCATT
1 -CAATATACTTACCATT
3183718 ATTGCTTATT
Statistics
Matches: 99, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
44 42 0.42
45 57 0.58
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (44 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
Found at i:3184842 original size:29 final size:30
Alignment explanation
Indices: 3184780--3184842 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3184770 TTCCCAACTT
* * * **
3184780 TTTCCAAAATTACAAATTGGTCCCTTAACT
1 TTTCAAAAAATACAAAATGGTCCCTTAAAA
3184810 TTTCAAAAAATACAAAATGGTCCC-TAAAA
1 TTTCAAAAAATACAAAATGGTCCCTTAAAA
3184839 TTTC
1 TTTC
3184843 TAAGGATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (30 bp):
TTTCAAAAAATACAAAATGGTCCCTTAAAA
Found at i:3187716 original size:15 final size:13
Alignment explanation
Indices: 3187685--3187804 Score: 73
Period size: 14 Copynumber: 8.5 Consensus size: 13
3187675 ATCTCTCATC
**
3187685 TTTTTTTCTTCCA
1 TTTTTTTCTTTTA
3187698 TTTTTTTTCTTTTA
1 -TTTTTTTCTTTTA
3187712 CTTTTTTTCTATTTA
1 -TTTTTTTCT-TTTA
*
3187727 TTTTTTTCTTTGTC
1 TTTTTTTCTTT-TA
3187741 TTTTTTGTCTTTT-
1 TTTTTT-TCTTTTA
*
3187754 TGTCTTTTTCTTCTTT
1 T-T-TTTTTCTT-TTA
3187770 TTCTTCTTTCTTTT-
1 TT-TT-TTTCTTTTA
*
3187784 TGTTTTCTTCTTCTA
1 T-TTTT-TTCTTTTA
3187799 TTTTTT
1 TTTTTT
3187805 AAGCTCTTAT
Statistics
Matches: 90, Mismatches: 5, Indels: 23
0.76 0.04 0.19
Matches are distributed among these distances:
13 5 0.06
14 55 0.61
15 23 0.26
16 7 0.08
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTTTTCTTTTA
Found at i:3187749 original size:9 final size:9
Alignment explanation
Indices: 3187735--3187771 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3187725 TATTTTTTTC
3187735 TTTGTCTTT
1 TTTGTCTTT
3187744 TTTGTC-TT
1 TTTGTCTTT
3187752 TTTGTCTTT
1 TTTGTCTTT
3187761 TTCT-TCTTT
1 TT-TGTCTTT
3187770 TT
1 TT
3187772 CTTCTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.31
9 17 0.65
10 1 0.04
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (9 bp):
TTTGTCTTT
Found at i:3187753 original size:23 final size:23
Alignment explanation
Indices: 3187718--3187804 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
3187708 TTTACTTTTT
* *
3187718 TTCTATTTATTTTTTTCTTTGTC
1 TTCTTTTTCTTTTTTTCTTTGTC
* *
3187741 TT-TTTTGTCTTTTTGTCTTTTTC
1 TTCTTTT-TCTTTTTTTCTTTGTC
*
3187764 TTCTTTTTCTTCTTTCTT-TTTGTT
1 TTCTTTTTCTT-TTT-TTCTTTGTC
*
3187788 TTCTTCTTCTATTTTTT
1 TTCTTTTTCT-TTTTTT
3187805 AAGCTCTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
22 3 0.06
23 23 0.45
24 23 0.45
25 2 0.04
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (23 bp):
TTCTTTTTCTTTTTTTCTTTGTC
Found at i:3187757 original size:17 final size:17
Alignment explanation
Indices: 3187735--3187771 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3187725 TATTTTTTTC
3187735 TTTGTCTTTTT-TGTCTT
1 TTTGTCTTTTTCT-TCTT
3187752 TTTGTCTTTTTCTTCTT
1 TTTGTCTTTTTCTTCTT
3187769 TTT
1 TTT
3187772 CTTCTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (17 bp):
TTTGTCTTTTTCTTCTT
Found at i:3187765 original size:14 final size:14
Alignment explanation
Indices: 3187699--3187795 Score: 88
Period size: 14 Copynumber: 6.7 Consensus size: 14
3187689 TTTCTTCCAT
*
3187699 TTTTTTTCTTTTAC
1 TTTTTTTCTTTTTC
* *
3187713 TTTTTTTCTATTTA
1 TTTTTTTCTTTTTC
*
3187727 TTTTTTTCTTTGTC
1 TTTTTTTCTTTTTC
3187741 TTTTTTGTCTTTTTGTC
1 TTTTTT-TC-TTTT-TC
3187758 TTTTTCTTCTTTTTC
1 TTTTT-TTCTTTTTC
* *
3187773 -TTCTTTCTTTTTG
1 TTTTTTTCTTTTTC
*
3187786 TTTTCTTCTT
1 TTTTTTTCTT
3187796 CTATTTTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
13 8 0.12
14 38 0.57
15 4 0.06
16 7 0.10
17 9 0.13
18 1 0.01
ACGTcount: A:0.03, C:0.14, G:0.04, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:3190649 original size:44 final size:45
Alignment explanation
Indices: 3190536--3190710 Score: 264
Period size: 44 Copynumber: 3.9 Consensus size: 45
3190526 AATTTCTTAT
* * *
3190536 CAATTTACTTACCATTTATCTCATAAGCTGGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
3190581 CAATTTACTTACCATTTATCCCATAAGCTCGTAAGCGTATTTTA-
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
3190625 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* * *
3190670 CAATATACTTTCC-GTTATTCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
3190711 GCATGCATAC
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
44 68 0.56
45 53 0.44
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:3190651 original size:89 final size:88
Alignment explanation
Indices: 3190536--3190710 Score: 269
Period size: 89 Copynumber: 2.0 Consensus size: 88
3190526 AATTTCTTAT
* * * * *
3190536 CAATTTACTTACCATTTATCTCATAAGCTGGTAAGCTTATTTTACCAATTTACTTACCATTTATC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACC-GTTATC
3190601 CCATAAGCTCGTAAGCGTATTTTA
65 CCATAAGCTCGTAAGCGTATTTTA
* *
3190625 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTTCCGTTATTC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCGTTATCC
*
3190690 CATAAGCTCGTAAGCTTATTT
66 CATAAGCTCGTAAGCGTATTT
3190711 GCATGCATAC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 25 0.32
89 53 0.68
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (88 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCGTTATCC
CATAAGCTCGTAAGCGTATTTTA
Found at i:3214251 original size:19 final size:20
Alignment explanation
Indices: 3214223--3214273 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
3214213 GCCAAGAGCT
*
3214223 TGTATCTTCATT-AAAATCA
1 TGTATTTTCATTAAAAATCA
3214242 TGTATTTTCATTAAAAAAATCA
1 TGTATTTTCATT--AAAAATCA
3214264 TGTATTTTCA
1 TGTATTTTCA
3214274 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.39
22 17 0.61
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (20 bp):
TGTATTTTCATTAAAAATCA
Done.