Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 140 of 168
Found at i:41077445 original size:85 final size:84
Alignment explanation
Indices: 41077348--41077558 Score: 264
Period size: 85 Copynumber: 2.5 Consensus size: 84
41077338 CGTTTGTGAA
* * * * * * * *
41077348 AAAGCGCCGCTAAAGTACGTGATCTATAGCTGCGTTTTTATTTAATCGCCGCTAAAGAACATGAT
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTATTCAAGCGCCGCTAAAGAACATGAC
*
41077413 CTTTAGTGGCATTTAATTTT-
66 CTTTAGAGGCATTT--TTTTC
*
41077433 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTGGTT-TTCAAGCGCCGCTAAAGAACATG
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT--TTATTCAAGCGCCGCTAAAGAACATG
*
41077497 ACCTTTAGAGGCGTTTTTTTC
64 ACCTTTAGAGGCATTTTTTTC
*
41077518 CAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTAT
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTAT
41077559 CTGTAAACGC
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
83 2 0.02
84 5 0.05
85 66 0.61
86 34 0.31
87 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (84 bp):
AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTATTCAAGCGCCGCTAAAGAACATGAC
CTTTAGAGGCATTTTTTTC
Found at i:41077447 original size:43 final size:41
Alignment explanation
Indices: 41077349--41077556 Score: 218
Period size: 43 Copynumber: 4.9 Consensus size: 41
41077339 GTTTGTGAAA
* * * * ** * *
41077349 AAGCGCCGCTAAAGTACGTGATCTATAGCTGCGTTTTTATTT
1 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCATTTTT-TTC
* * * *
41077391 AATCGCCGCTAAAGAACATGATCTTTAGTGGCATTTAATTTTA
1 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCATTT--TTTTC
*
41077434 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTGGTTTTC
1 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCATTT--TTTTC
*
41077477 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCATTTTTTT-C
* *
41077519 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCATTTTT
41077557 ATCTGTAAAC
Statistics
Matches: 146, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.03
42 67 0.46
43 73 0.50
44 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGACCTTTAGAGGCATTTTTTTC
Found at i:41079104 original size:94 final size:94
Alignment explanation
Indices: 41078998--41079198 Score: 242
Period size: 94 Copynumber: 2.1 Consensus size: 94
41078988 TAAAATCAAC
* * * * * *
41078998 TGTGATCATAAATCATCTAGTTGTTAGGAGTAACGATAGTAAATCAACTAACTC-GTAGAAGATT
1 TGTGATCGTAAATCAACGAATTGTTAGAAGTAACGATAATAAATCAACTAACTCAG-AGAAGATT
* * *
41079062 GTTTATGATCGTAAATCAATGAACTTAGGT
65 GTTCATGACCGTAAATCAATAAACTTAGGT
* ** *
41079092 TGTGATCGTAAATCAACGAATTGTTTGAAGTAGTGATAATAAATCAGCTAACTCAGAGAAGATTG
1 TGTGATCGTAAATCAACGAATTGTTAGAAGTAACGATAATAAATCAACTAACTCAGAGAAGATTG
*
41079157 TTCATGACCGTCAATCAATAAACTTAGGT
66 TTCATGACCGTAAATCAATAAACTTAGGT
* *
41079186 TATTATCGTAAAT
1 TGTGATCGTAAAT
41079199 TAATGAGTCT
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 89 0.99
95 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (94 bp):
TGTGATCGTAAATCAACGAATTGTTAGAAGTAACGATAATAAATCAACTAACTCAGAGAAGATTG
TTCATGACCGTAAATCAATAAACTTAGGT
Found at i:41090673 original size:9 final size:9
Alignment explanation
Indices: 41090660--41090726 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
41090650 TTTGGGTAAA
*
41090660 AATTAACCA
1 AATTAACCG
41090669 AATTAACCG
1 AATTAACCG
*
41090678 AATTACCCG
1 AATTAACCG
41090687 AATTAACCG
1 AATTAACCG
*
41090696 AATTACCCG
1 AATTAACCG
**
41090705 AATTAACTA
1 AATTAACCG
41090714 AATTAACCG
1 AATTAACCG
41090723 AATT
1 AATT
41090727 GAATCACTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:41093970 original size:14 final size:14
Alignment explanation
Indices: 41093951--41093980 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41093941 ATAATCAAAA
41093951 TTCATGTGTATAAT
1 TTCATGTGTATAAT
41093965 TTCATGTGTATAAT
1 TTCATGTGTATAAT
41093979 TT
1 TT
41093981 AATTAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTCATGTGTATAAT
Found at i:41103171 original size:47 final size:47
Alignment explanation
Indices: 41103117--41103212 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
41103107 CATCATAAGG
41103117 ACCTCATATTTAAAAAGCCATGTCAATTCAGCACTTTAACAAATGGC
1 ACCTCATATTTAAAAAGCCATGTCAATTCAGCACTTTAACAAATGGC
41103164 ACCTCATATTTAAAAAGCCATGTCAATTCAGCACTTTAACAAATGGC
1 ACCTCATATTTAAAAAGCCATGTCAATTCAGCACTTTAACAAATGGC
41103211 AC
1 AC
41103213 ACAACTTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (47 bp):
ACCTCATATTTAAAAAGCCATGTCAATTCAGCACTTTAACAAATGGC
Found at i:41107988 original size:33 final size:33
Alignment explanation
Indices: 41107951--41108023 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
41107941 AAAATATTAT
*
41107951 TTTTTTTAAATTAG-ATTTTGA-ATTGAGTTTGAA
1 TTTTTTTAAATT-GTA-TTTGATATTGAGTTTAAA
** *
41107984 TTTTTACAAATTGTATTTGATATTGGGTTTAAA
1 TTTTTTTAAATTGTATTTGATATTGAGTTTAAA
41108017 TTTTTTT
1 TTTTTTT
41108024 TATTGTGGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (33 bp):
TTTTTTTAAATTGTATTTGATATTGAGTTTAAA
Found at i:41117905 original size:193 final size:193
Alignment explanation
Indices: 41117632--41118399 Score: 865
Period size: 193 Copynumber: 4.0 Consensus size: 193
41117622 CAAGGTAAAC
* ** * * *
41117632 AAAACTTGGAAACTAATTTTTATA-CTTAATCAAGCACGATCATCTATTAACTTTCCCAATCGTG
1 AAAACTTGAAAACTAATCCTTATACCTT-GTCAAGTACGATCATCTATTAACTTTCCCAATCGTA
** * * * *
41117696 TAATTCATATTGTATTAAATGAGATATATATTAATTGACTTAAGATTCATGTATCATCTAACCAA
65 TAATTTGTATTGTATTATATGAGACATATATTAGTTGACTTAAGATTCATATATCATCTAACCAA
* * *
41117761 AATATAAGTTTAAATTTGCTTTCAAGTGTGTT-TTACGTGGAAGTTACATTGATGCTAACAAAAG
130 AATATAAGTTT-AATTTGCTTTCAAGTATGTTGTT-TGTGGAAATTACATTGATGCTAACAAAAG
41117825 A
193 A
* * * * * * *
41117826 AAAGCTTAAAAACTAATCCTTATATCTTGTCAAGTACGACCATGTGTTAA-TTTTCCAATCGTAT
1 AAAACTTGAAAACTAATCCTTATACCTTGTCAAGTACGATCATCTATTAACTTTCCCAATCGTAT
** *
41117890 AATTTGTATTGTATTATATGAGACATATATTAGCCGACTTAAGATTCATATATCATCTACCCAAA
66 AATTTGTATTGTATTATATGAGACATATATTAGTTGACTTAAGATTCATATATCATCTAACCAAA
*
41117955 ATACAAGTTTAATTTGCTTTC-AGTTATGTTGTTTGTGG--A--A-ATTGATGCTAACAAAAGA
131 ATATAAGTTTAATTTGCTTTCAAG-TATGTTGTTTGTGGAAATTACATTGATGCTAACAAAAGA
* * * * *
41118013 AAAACTTGCAAACTAATCCTCATACCCTGTAAAGTACGATCATCTATTAACTTTCCCAATGGTAT
1 AAAACTTGAAAACTAATCCTTATACCTTGTCAAGTACGATCATCTATTAACTTTCCCAATCGTAT
* * *
41118078 AATTTGTATTGTATTATATGAGAC--ATGTTAGTTAACTTAAGATTCATATATCATCTGACCAAA
66 AATTTGTATTGTATTATATGAGACATATATTAGTTGACTTAAGATTCATATATCATCTAACCAAA
** * * * **
41118141 GGATAAGTTTAATTTGCTTTCAACTATGTTGTTTGTGAAAATTGCATTGATGCTGGCAAAAGA
131 ATATAAGTTTAATTTGCTTTCAAGTATGTTGTTTGTGGAAATTACATTGATGCTAACAAAAGA
* * * * **
41118204 AAAACTTGAAAATTAATCCTTATACCTTGTCAAGCACAATCATCTATTAACTTTCTCAATTATAT
1 AAAACTTGAAAACTAATCCTTATACCTTGTCAAGTACGATCATCTATTAACTTTCCCAATCGTAT
* * * * *
41118269 ATATAATCTGTATTGTATTATATGAAACATATATTAGTTGACTTAATATTCACATATCAACTATC
66 A-AT--T-TGTATTGTATTATATGAGACATATATTAGTTGACTTAAGATTCATATATCATCTAAC
* * * *
41118334 CAAAATATAAGTTTAATTTGCTTTCAACTGTGTTTTTTTTGTGGAAATTACATTGATGCTACCAA
127 CAAAATATAAGTTTAATTTGCTTTCAA--GTATGTTGTTTGTGGAAATTACATTGATGCTAACAA
41118399 A
190 A
41118400 GTAAAAAGTA
Statistics
Matches: 477, Mismatches: 79, Indels: 31
0.81 0.13 0.05
Matches are distributed among these distances:
186 64 0.13
187 59 0.12
188 38 0.08
191 74 0.16
192 22 0.05
193 79 0.17
194 37 0.08
195 22 0.05
197 53 0.11
199 29 0.06
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (193 bp):
AAAACTTGAAAACTAATCCTTATACCTTGTCAAGTACGATCATCTATTAACTTTCCCAATCGTAT
AATTTGTATTGTATTATATGAGACATATATTAGTTGACTTAAGATTCATATATCATCTAACCAAA
ATATAAGTTTAATTTGCTTTCAAGTATGTTGTTTGTGGAAATTACATTGATGCTAACAAAAGA
Found at i:41118351 original size:383 final size:380
Alignment explanation
Indices: 41117667--41118359 Score: 933
Period size: 378 Copynumber: 1.8 Consensus size: 380
41117657 TTAATCAAGC
* *
41117667 ACGATCATCTATTAACTTTCCCAATCGTGTAATTCATATTGTATTAAATGAGATATATATTAATT
1 ACGATCATCTATTAACTTTCCCAATCGTATAATTCATATTGTATTAAATGAGA-ACATATTAATT
* * * * *
41117732 GACTTAAGATTCATGTATCATCTAACCAAAATATAAGTTTAAATTTGCTTTCAAGTGTGTTTTAC
65 AACTTAAGATTCATATATCATCTAACCAAAAGATAAGTTTAAATTTGCTTTCAACTATGTTTTAC
* * * * *
41117797 GTGGAAGTTACATTGATGCTAACAAAAGAAAAGCTTAAAAACTAATCCTTATATCTTGTCAAGTA
130 GTGAAAATTACATTGATGCTAACAAAAGAAAAACTTAAAAACTAATCCTTATACCTTGTCAAGCA
* * * * * *
41117862 CGACCATGTGTTAATTTTCCAATCGTATAATTTGTATTGTATTATATGAGACATATATTAGCCGA
195 CAACCATCTATTAACTTTCCAATCATATAATTTGTATTGTATTATATGAAACATATATTAGCCGA
* *
41117927 CTTAAGATTCATATATCATCTACCCAAAATACAAGTTTAATTTGCTTTCAGTTATGTTGTTTGTG
260 CTTAAGATTCACATATCAACTACCCAAAATACAAGTTTAATTTGCTTTCAGTTATGTTGTTTGTG
41117992 GAAATTGATGCTAACAAAAGAAAAACTTGCAAACTAATCCTCATACCCTGTAAAGT
325 GAAATTGATGCTAACAAAAGAAAAACTTGCAAACTAATCCTCATACCCTGTAAAGT
* ** * * *
41118048 ACGATCATCTATTAACTTTCCCAATGGTATAATTTGTATTGTATTATATGAG-ACATGTTAGTTA
1 ACGATCATCTATTAACTTTCCCAATCGTATAATTCATATTGTATTAAATGAGAACATATTAATTA
* * *
41118112 ACTTAAGATTCATATATCATCTGACCAAAGGATAAGTTT-AATTTGCTTTCAACTATGTTGTT-T
66 ACTTAAGATTCATATATCATCTAACCAAAAGATAAGTTTAAATTTGCTTTCAACTATGTT-TTAC
* ** * *
41118175 GTGAAAATTGCATTGATGCTGGCAAAAGAAAAACTTGAAAATTAATCCTTATACCTTGTCAAGCA
130 GTGAAAATTACATTGATGCTAACAAAAGAAAAACTTAAAAACTAATCCTTATACCTTGTCAAGCA
* *
41118240 CAATCATCTATTAACTTTCTCAATTATATATATAATCTGTATTGTATTATATGAAACATATATTA
195 CAACCATCTATTAACTTTC-CAATCATATA-AT--T-TGTATTGTATTATATGAAACATATATTA
** * * *
41118305 GTTGACTTAATATTCACATATCAACTATCCAAAATATAAGTTTAATTTGCTTTCA
255 GCCGACTTAAGATTCACATATCAACTACCCAAAATACAAGTTTAATTTGCTTTCA
41118360 ACTGTGTTTT
Statistics
Matches: 265, Mismatches: 41, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
378 87 0.33
379 53 0.20
380 2 0.01
381 47 0.18
382 1 0.00
383 75 0.28
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (380 bp):
ACGATCATCTATTAACTTTCCCAATCGTATAATTCATATTGTATTAAATGAGAACATATTAATTA
ACTTAAGATTCATATATCATCTAACCAAAAGATAAGTTTAAATTTGCTTTCAACTATGTTTTACG
TGAAAATTACATTGATGCTAACAAAAGAAAAACTTAAAAACTAATCCTTATACCTTGTCAAGCAC
AACCATCTATTAACTTTCCAATCATATAATTTGTATTGTATTATATGAAACATATATTAGCCGAC
TTAAGATTCACATATCAACTACCCAAAATACAAGTTTAATTTGCTTTCAGTTATGTTGTTTGTGG
AAATTGATGCTAACAAAAGAAAAACTTGCAAACTAATCCTCATACCCTGTAAAGT
Found at i:41123192 original size:37 final size:37
Alignment explanation
Indices: 41123134--41123362 Score: 304
Period size: 37 Copynumber: 6.0 Consensus size: 37
41123124 TACGTATGAT
41123134 CACTTATCAC--TGTC-C-TGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
41123167 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
41123204 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
41123241 CACTTATCACTTTGTTTCTTGATCAGATAAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGAT-AAGTGTAGC
41123279 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
41123316 TAAAGCTATTACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 -----C----ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
41123362 C
1 C
41123363 GAAGCTATCA
Statistics
Matches: 175, Mismatches: 7, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
33 9 0.05
35 3 0.02
36 1 0.01
37 89 0.51
38 36 0.21
41 1 0.01
42 1 0.01
46 35 0.20
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:41123233 original size:74 final size:75
Alignment explanation
Indices: 41123134--41123315 Score: 320
Period size: 75 Copynumber: 2.5 Consensus size: 75
41123124 TACGTATGAT
41123134 CACTTATCAC--TGTC-C-TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGAT
41123195 -AAGTGTAGC
66 AAAGTGTAGC
*
41123204 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCTTGATCAGAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGAT
41123269 AAAGTGTAGC
66 AAAGTGTAGC
41123279 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
41123316 TAAAGCTATT
Statistics
Matches: 106, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
70 10 0.09
72 4 0.04
73 1 0.01
74 45 0.42
75 46 0.43
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (75 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGAT
AAAGTGTAGC
Found at i:41123330 original size:46 final size:46
Alignment explanation
Indices: 41123279--41123652 Score: 304
Period size: 46 Copynumber: 7.6 Consensus size: 46
41123269 AAAGTGTAGC
* * **
41123279 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
41123325 TACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
41123371 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * * * *
41123423 CACTTATCACTTTCCACTTTCCACTTG-TCACTTGATCAG-ATAAG-TGTAGCTGAAG
1 CACTTATCAC-TT----TGT-CACTTGATCA---GATAAGTAT-AGCCGAAGCT--AT
**
41123478 CTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 C-A-CTT--ATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
41123528 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
41123574 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
41123626 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
41123653 AGTACTCAAA
Statistics
Matches: 270, Mismatches: 28, Indels: 60
0.75 0.08 0.17
Matches are distributed among these distances:
46 117 0.43
47 1 0.00
48 2 0.01
49 2 0.01
50 5 0.02
51 12 0.04
52 96 0.36
53 12 0.04
54 12 0.04
55 2 0.01
56 1 0.00
57 1 0.00
58 2 0.01
59 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:41123392 original size:52 final size:52
Alignment explanation
Indices: 41123326--41123646 Score: 378
Period size: 46 Copynumber: 6.2 Consensus size: 52
41123316 TAAAGCTATT
* *
41123326 ACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
1 ACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
*
41123379 ACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
* *
41123431 ACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATC
1 AC--T----TTT-CACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
41123490 AC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
*
41123536 AC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
* * ** *
41123582 ACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
41123634 ACTTTGTCACTTG
1 ACTTT-TCACTTG
41123647 ATCAGAAGTA
Statistics
Matches: 240, Mismatches: 14, Indels: 28
0.85 0.05 0.10
Matches are distributed among these distances:
46 88 0.37
50 1 0.00
52 86 0.36
53 14 0.06
54 1 0.00
58 3 0.01
59 47 0.20
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
Found at i:41123441 original size:59 final size:58
Alignment explanation
Indices: 41123368--41123494 Score: 218
Period size: 59 Copynumber: 2.2 Consensus size: 58
41123358 TAGCCGAAGC
*
41123368 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTT-TCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
41123427 TATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTT-CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
41123486 TATCACTTT
1 TATCACTTT
41123495 GTCACTTGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 1 0.02
59 64 0.98
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (58 bp):
TATCACTTTCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:41126601 original size:24 final size:24
Alignment explanation
Indices: 41126574--41126624 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
41126564 TGCGAGCATA
*
41126574 TAACGGGTAGCTCCAAAGAGTACT
1 TAACGGGTAGCTCCAAAGAGCACT
*
41126598 TAACGGGTAGCTCCGAAGAGCACT
1 TAACGGGTAGCTCCAAAGAGCACT
41126622 TAA
1 TAA
41126625 TCAGAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGAGCACT
Found at i:41126703 original size:25 final size:24
Alignment explanation
Indices: 41126641--41126716 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 24
41126631 AGAACCGGAT
* * *
41126641 AGCCATATAATAGGAAGTTCAAACG
1 AGCCATAT-ATGGGAAGCTCAAAAG
* *
41126666 AGCAATA-ACGGGAAGCTCACAAAG
1 AGCCATATATGGGAAGCTCA-AAAG
* *
41126690 AGCCATATATGGGACGCTCATAAG
1 AGCCATATATGGGAAGCTCAAAAG
41126714 AGC
1 AGC
41126717 TGCGGTGTGC
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
23 9 0.22
24 15 0.38
25 16 0.40
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.16
Consensus pattern (24 bp):
AGCCATATATGGGAAGCTCAAAAG
Found at i:41126803 original size:25 final size:25
Alignment explanation
Indices: 41126775--41126837 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
41126765 CGAAGACCTA
41126775 TTAACGGGAAGCTCACAAAAACCAT
1 TTAACGGGAAGCTCACAAAAACCAT
* * *
41126800 TTAACGAGAAGCTCGCAAGAACCAT
1 TTAACGGGAAGCTCACAAAAACCAT
41126825 TTAACGGGAAGCT
1 TTAACGGGAAGCT
41126838 TGAGAAGGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (25 bp):
TTAACGGGAAGCTCACAAAAACCAT
Found at i:41129430 original size:17 final size:17
Alignment explanation
Indices: 41129405--41129441 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
41129395 TTAGACTTGG
41129405 ATTGAGAAAATAATTTA
1 ATTGAGAAAATAATTTA
* *
41129422 ATTGGGAAATTAATTTA
1 ATTGAGAAAATAATTTA
41129439 ATT
1 ATT
41129442 AATTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (17 bp):
ATTGAGAAAATAATTTA
Found at i:41133010 original size:14 final size:13
Alignment explanation
Indices: 41132991--41133041 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
41132981 ATATGTTATT
41132991 TTTTTATAACATTA
1 TTTTTATAA-ATTA
41133005 TTTTTATAATATTA
1 TTTTTATAA-ATTA
*
41133019 TTATTTTTATAATT-
1 TT-TTTATA-AATTA
41133033 TTTTTATAA
1 TTTTTATAA
41133042 GCTTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.03
13 5 0.16
14 17 0.53
15 8 0.25
16 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTATAAATTA
Found at i:41143600 original size:3 final size:3
Alignment explanation
Indices: 41143592--41143622 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41143582 TTCAAACAAA
41143592 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
41143623 AGTAGTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:41156784 original size:55 final size:55
Alignment explanation
Indices: 41156713--41156866 Score: 290
Period size: 55 Copynumber: 2.8 Consensus size: 55
41156703 CTTATTATCA
*
41156713 TTTCTAGTAATGGATGTTGAAGCATATCTTTAAAGAAACAAATCCAGATACATGG
1 TTTCCAGTAATGGATGTTGAAGCATATCTTTAAAGAAACAAATCCAGATACATGG
41156768 TTTCCAGTAATGGATGTTGAAGCATATCTTTAAAGAAACAAATCCAGATACATGG
1 TTTCCAGTAATGGATGTTGAAGCATATCTTTAAAGAAACAAATCCAGATACATGG
*
41156823 TTTCCAGTAATGGATGTTGAAGCATATCTTTAAGGAAACAAATC
1 TTTCCAGTAATGGATGTTGAAGCATATCTTTAAAGAAACAAATC
41156867 GTGGGATTAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 97 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (55 bp):
TTTCCAGTAATGGATGTTGAAGCATATCTTTAAAGAAACAAATCCAGATACATGG
Found at i:41166056 original size:23 final size:23
Alignment explanation
Indices: 41166030--41166075 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41166020 AATGATAGTC
41166030 TAAATA-CTAAAATAAAACAAATT
1 TAAATATC-AAAATAAAACAAATT
* *
41166053 TAAATATCAAAGTAAAAGAAATT
1 TAAATATCAAAATAAAACAAATT
41166076 ATATAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (23 bp):
TAAATATCAAAATAAAACAAATT
Found at i:41172890 original size:31 final size:30
Alignment explanation
Indices: 41172854--41172914 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41172844 GTCCAGTCAC
*
41172854 TTAAATAAAAAGTTTCGAATAATTTAGTGAT
1 TTAAATAAAAA-TTTCGAATAATTTAATGAT
* * *
41172885 TTAAATGAAAATTTTGAATAGTTTAATGAT
1 TTAAATAAAAATTTCGAATAATTTAATGAT
41172915 GATTTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.41
Consensus pattern (30 bp):
TTAAATAAAAATTTCGAATAATTTAATGAT
Found at i:41175527 original size:55 final size:55
Alignment explanation
Indices: 41175438--41175548 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
41175428 TGATGACTGA
*
41175438 TATTGATTCATTGTATAGCATTCCTTGATGAAAATACTGAAGAACTATGTGTTTT
1 TATTGATTCATTGTATAGCATTCCTTGATGAAAATACTGAAGAACTATGTATTTT
* *
41175493 TATTTATTCATTGTATAGCATTCCTTGATGAAAATGCTGAAGAACTATGTATTTT
1 TATTGATTCATTGTATAGCATTCCTTGATGAAAATACTGAAGAACTATGTATTTT
41175548 T
1 T
41175549 TTCCTACAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (55 bp):
TATTGATTCATTGTATAGCATTCCTTGATGAAAATACTGAAGAACTATGTATTTT
Found at i:41178331 original size:22 final size:21
Alignment explanation
Indices: 41178286--41178334 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
41178276 AATAAGAAAG
*
41178286 GAAAA-AA-AGAGGAAAAATA
1 GAAAAGAATAGAGGAAAAAAA
41178305 GAAAAGAATAGAGGAAAAAAAA
1 GAAAAGAATAGAGG-AAAAAAA
*
41178327 TAAAAGAA
1 GAAAAGAA
41178335 CTAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 2 0.08
21 5 0.20
22 13 0.52
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (21 bp):
GAAAAGAATAGAGGAAAAAAA
Found at i:41184776 original size:16 final size:15
Alignment explanation
Indices: 41184757--41184808 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
41184747 AAATCTAGAA
41184757 AAAAATATAAATTATT
1 AAAAATA-AAATTATT
**
41184773 -AAAATAAAATTTACA
1 AAAAATAAAA-TTATT
41184788 AAAAATAAAATTATT
1 AAAAATAAAATTATT
41184803 GAAAAA
1 -AAAAA
41184809 AATTAGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 3 0.10
15 12 0.41
16 14 0.48
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAAATAAAATTATT
Found at i:41184799 original size:30 final size:30
Alignment explanation
Indices: 41184756--41184812 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41184746 AAAATCTAGA
41184756 AAAAAATATAAATTATTAAAATAAAATTTAC
1 AAAAAATATAAATTATTAAAA-AAAATTTAC
*
41184787 AAAAAATA-AAATTATTGAAAAAAATT
1 AAAAAATATAAATTATTAAAAAAAATT
41184813 AGTTGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 6 0.24
30 11 0.44
31 8 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (30 bp):
AAAAAATATAAATTATTAAAAAAAATTTAC
Found at i:41184807 original size:15 final size:15
Alignment explanation
Indices: 41184758--41184820 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
41184748 AATCTAGAAA
41184758 AAAATATAAATTATT-
1 AAAATA-AAATTATTG
***
41184773 AAAATAAAATTTACAA
1 AAAATAAAA-TTATTG
41184789 AAAATAAAATTATTG
1 AAAATAAAATTATTG
41184804 -AAA-AAAATTAGTTG
1 AAAATAAAATTA-TTG
41184818 AAA
1 AAA
41184821 TTAATAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 7 0.18
14 9 0.23
15 14 0.36
16 9 0.23
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (15 bp):
AAAATAAAATTATTG
Found at i:41185083 original size:23 final size:23
Alignment explanation
Indices: 41185049--41185120 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
41185039 TACTTTGATT
41185049 TTTTAAAA-TTTATAATTATATA
1 TTTTAAAATTTTATAATTATATA
**
41185071 TTTTAAAATTTTATAAAAAATATA
1 TTTTAAAATTTTAT-AATTATATA
* *
41185095 TTTCAAATTTATTATACATTATATA
1 TTTTAAAATT-TTATA-ATTATATA
41185120 T
1 T
41185121 GATTTTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 8 0.20
23 5 0.12
24 16 0.40
25 11 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTAAAATTTTATAATTATATA
Found at i:41185093 original size:22 final size:23
Alignment explanation
Indices: 41185049--41185104 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
41185039 TACTTTGATT
* *
41185049 TTTTAAAA-TTTATAATTATATA
1 TTTTAAAATTTTATAATAAAATA
41185071 TTTTAAAATTTTATAA-AAAATA
1 TTTTAAAATTTTATAATAAAATA
*
41185093 TATTTCAAATTT
1 T-TTTAAAATTT
41185105 ATTATACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTAAAATTTTATAATAAAATA
Found at i:41186190 original size:33 final size:32
Alignment explanation
Indices: 41186144--41186207 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
41186134 TTTAAAAAAA
41186144 TTTACTTCCTCAAACCTCC-AATT-TTTTTCTT
1 TTTACTTCCTCAAACC-CCAAATTCTTTTTCTT
41186175 TTTACTTTCCCTCAAACCCCAAATTCTTTTTCT
1 TTTAC-TT-CCTCAAACCCCAAATTCTTTTTCT
41186208 CCAAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 5 0.17
32 4 0.14
33 13 0.45
34 7 0.24
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.48
Consensus pattern (32 bp):
TTTACTTCCTCAAACCCCAAATTCTTTTTCTT
Found at i:41193896 original size:51 final size:52
Alignment explanation
Indices: 41193831--41193930 Score: 159
Period size: 51 Copynumber: 1.9 Consensus size: 52
41193821 ATACGTCGAG
*
41193831 TTTTAAAGATAAAATCATATTATCATATTTG-AA-AAGTAAATTGATCGATT
1 TTTTAAAGACAAAATCATATTATCATATTTGTAATAAGTAAATTGATCGATT
*
41193881 TTTTAAAAGACAAAATGATATTATCATATTTGTAATAAGTAAATTGATCG
1 TTTT-AAAGACAAAATCATATTATCATATTTGTAATAAGTAAATTGATCG
41193931 GTCGGTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 4 0.09
51 25 0.56
52 2 0.04
53 14 0.31
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (52 bp):
TTTTAAAGACAAAATCATATTATCATATTTGTAATAAGTAAATTGATCGATT
Found at i:41199373 original size:43 final size:43
Alignment explanation
Indices: 41199312--41199595 Score: 355
Period size: 43 Copynumber: 6.7 Consensus size: 43
41199302 TATGATTTCA
*
41199312 TGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACG
41199355 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACG
*
41199398 TGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACG
*
41199441 TGTAAGACCACGTCTGGAACGTTGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACG
* * ** *
41199484 TGTAAGACCATGTCTGGAACACTGGCATCGTA-TT-TGATT-CG
1 TGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTTTACG
** * ** * *
41199525 TGTAAGACC-CTGTCTGGGACAG-TGTAATTGA-TATAAGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTTTACG
41199568 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
41199596 TGTACGATAT
Statistics
Matches: 215, Mismatches: 18, Indels: 16
0.86 0.07 0.06
Matches are distributed among these distances:
40 2 0.01
41 25 0.12
42 9 0.04
43 177 0.82
44 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACG
Found at i:41203629 original size:458 final size:457
Alignment explanation
Indices: 41202254--41203632 Score: 2380
Period size: 458 Copynumber: 3.0 Consensus size: 457
41202244 AGCTATGGTT
* * *
41202254 ATACACCTTGTAATCCCCAAATGACCTTATTGCCATCGCGGCGTCGCTCCTTAGAGCTTACTGAT
1 ATACACCTTGTAATCCCCAAATGACCTTATCG-CGTCGCGGCGTCGCTCCTTAGAGCTTACTAAT
*
41202319 TGTCGTTGTGGTGTTGCTCTACGAAACTTAATAGCCATCAATATCGTCTTATCTCATATCAACCT
65 TGTCGTTGTGGTGTTGCTCTACGAAACTTAATAGCCGTCAATATCGTCTTATCTCATATCAACCT
*
41202384 TGATGCTCGAACACCAAAGTGTCCCCCAGAGCTTCGCCTATTACGGTTTGCTCCTAGCAATCCCG
130 TGATGCTCGAACACCAAAGTGTCCCCCAGAGCTTCGCCCATTACGGTTTGCTCCTAGCAATCCCG
*
41202449 GATGGTGGAATCGTAATGGAATTTCAATTTCTTTTTTCCATATTCCTCCACCCATTCCTCCACTT
195 GATGGTGGAATCGTAATGGAATTTCAATTTCTTTTTTCCATATTCCTCCACCTATTCCTCCACTT
41202514 ATCATCCTAATATTGATGCTCGAACACTGTAGTGTCCCCTCTGCAAGGCTCGGAGCTTCGTTTAT
260 ATCATCCTAATATTGATGCTCGAACACTGTAGTGTCCCCTCTGCAAGGCTCGGAGCTTCGTTTAT
* * *
41202579 CACGATTTTCACTTAGCAATACCGTATTGCGGTATTTAAAAGAACCACCCTTTTTCCCATCCTAA
325 CACGATTTGCACTCAGCAATACCGTATTGCGGTATTTAACAGAACCACCCTTTTTCCCATCCTAA
41202644 CTTCATCTAGCTTGTCGATGATTCCCTTCCATATTTCATAGACATTACATGCAAATTCATAAACT
390 CTTCATCTAGCTTGTCGATGATTCCCTTCCATATTTCATAGACATTACATGCAAATTCATAAACT
*
41202709 ATG
455 ACG
* * *
41202712 AGACACCATGTAATCCCCAAATGACCTTATCGCTGTCGCGACGTCGCTCCTTAGAGCTTACTAAT
1 ATACACCTTGTAATCCCCAAATGACCTTATCGC-GTCGCGGCGTCGCTCCTTAGAGCTTACTAAT
41202777 TGTCGTTGTGGTGTTGCTCTACGAAACTTAATAGCCGTCAATATCGTCTTATCTCATATCAACCT
65 TGTCGTTGTGGTGTTGCTCTACGAAACTTAATAGCCGTCAATATCGTCTTATCTCATATCAACCT
* * *
41202842 TGATGCTCAAACACCAAAGTGTCCCCAAGAGCTTCGCCCATTACGGTTTGCTCCTAGCAATCCCA
130 TGATGCTCGAACACCAAAGTGTCCCCCAGAGCTTCGCCCATTACGGTTTGCTCCTAGCAATCCCG
* *
41202907 GATGGTGGAATCGTAATGGAATTTCAATTTCTTTTTTCCATATTCCTTCTCCTATTCCTCCACTT
195 GATGGTGGAATCGTAATGGAATTTCAATTTCTTTTTTCCATATTCCTCCACCTATTCCTCCACTT
* * * *
41202972 ATCATTCTAATATTGATGCTCGAACACTGTAGTATCCCCTCTACAAGGCTTGGAGCTTCGTTTAT
260 ATCATCCTAATATTGATGCTCGAACACTGTAGTGTCCCCTCTGCAAGGCTCGGAGCTTCGTTTAT
*
41203037 CACGATTTGCACTCAGCAATACTGTATTGCGGTATTTAACAGAACCACCCTTTTTCCCATCCTAA
325 CACGATTTGCACTCAGCAATACCGTATTGCGGTATTTAACAGAACCACCCTTTTTCCCATCCTAA
* *
41203102 CTTCATCTAGCTTGTCGATGATTCCCTTCCATATTTTAGAGACATTACATGCAAATTCATAAACT
390 CTTCATCTAGCTTGTCGATGATTCCCTTCCATATTTCATAGACATTACATGCAAATTCATAAACT
41203167 ACG
455 ACG
*
41203170 ATACACCTTGTAATCCCCAAATGACCTTATCGTCGTTGCGGCGTCGCTCCTTAGAGCTTACTAAT
1 ATACACCTTGTAATCCCCAAATGACCTTATCG-CGTCGCGGCGTCGCTCCTTAGAGCTTACTAAT
*
41203235 TGTCGTTGTGGTGTTGCTCTACGAAACTTAATAGCCGTCAATTTCGTCTTATCTCATATCAACCT
65 TGTCGTTGTGGTGTTGCTCTACGAAACTTAATAGCCGTCAATATCGTCTTATCTCATATCAACCT
* * * *
41203300 TGATGCTCGAACACCAAAGTGTCCCCCTGAGTTTTGCCCATTACGGTTTGCTCCTATCAATCCCG
130 TGATGCTCGAACACCAAAGTGTCCCCCAGAGCTTCGCCCATTACGGTTTGCTCCTAGCAATCCCG
* *
41203365 GATGGTGGAATCGTAATAGAATTTCAATTTCTTTTTTCCATATTCCTCCGCCTATTCCTCCACTT
195 GATGGTGGAATCGTAATGGAATTTCAATTTCTTTTTTCCATATTCCTCCACCTATTCCTCCACTT
*
41203430 ATCATCCTAATATTGATGCTCGAACACTGTAGTGTCCCCTCTGCAAGGCTCGAAGCTTCGTTTAT
260 ATCATCCTAATATTGATGCTCGAACACTGTAGTGTCCCCTCTGCAAGGCTCGGAGCTTCGTTTAT
* * *
41203495 CATGGTTTGCACTCAGCAATACCGTATTGCTGTATTTAACAGAACCACCCTTTTTCCCATCCTAA
325 CACGATTTGCACTCAGCAATACCGTATTGCGGTATTTAACAGAACCACCCTTTTTCCCATCCTAA
* *
41203560 CTTCATCTAGCTTGTCGATGATTCCCTTCCATATTTCATAGACATTACATACTAATTCATAAACT
390 CTTCATCTAGCTTGTCGATGATTCCCTTCCATATTTCATAGACATTACATGCAAATTCATAAACT
41203625 ACG
455 ACG
41203628 ATACA
1 ATACA
41203633 ATGGCAGATA
Statistics
Matches: 866, Mismatches: 53, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
457 1 0.00
458 864 1.00
459 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.34
Consensus pattern (457 bp):
ATACACCTTGTAATCCCCAAATGACCTTATCGCGTCGCGGCGTCGCTCCTTAGAGCTTACTAATT
GTCGTTGTGGTGTTGCTCTACGAAACTTAATAGCCGTCAATATCGTCTTATCTCATATCAACCTT
GATGCTCGAACACCAAAGTGTCCCCCAGAGCTTCGCCCATTACGGTTTGCTCCTAGCAATCCCGG
ATGGTGGAATCGTAATGGAATTTCAATTTCTTTTTTCCATATTCCTCCACCTATTCCTCCACTTA
TCATCCTAATATTGATGCTCGAACACTGTAGTGTCCCCTCTGCAAGGCTCGGAGCTTCGTTTATC
ACGATTTGCACTCAGCAATACCGTATTGCGGTATTTAACAGAACCACCCTTTTTCCCATCCTAAC
TTCATCTAGCTTGTCGATGATTCCCTTCCATATTTCATAGACATTACATGCAAATTCATAAACTA
CG
Found at i:41205793 original size:29 final size:30
Alignment explanation
Indices: 41205734--41205791 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41205724 TCCGAGCCTT
*
41205734 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
41205764 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
41205792 AGAGTCGAGG
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:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:41206021 original size:13 final size:13
Alignment explanation
Indices: 41206003--41206034 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41205993 TTTCCAGCAA
41206003 TTATGAATTTATT
1 TTATGAATTTATT
41206016 TTATGAATTTATT
1 TTATGAATTTATT
*
41206029 TGATGA
1 TTATGA
41206035 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:41206240 original size:50 final size:50
Alignment explanation
Indices: 41206129--41206377 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
41206119 ATTTGGGTAA
*
41206129 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
* *
41206185 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* *
41206235 AGAGGTCCCATGTAAGACCATGTCTGGGTCATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * * *
41206285 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** *
41206335 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41206378 TGTTATTATC
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 97 0.55
51 36 0.21
55 2 0.01
56 40 0.23
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:41211340 original size:30 final size:30
Alignment explanation
Indices: 41211268--41211340 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
41211258 GAAAGTCGAG
* *
41211268 TTCCTATATATAAAATTCTTATTGTGACCAT
1 TTCC-ATATATAGAATTCTTATTGTAACCAT
*
41211299 TTCCATATATAGAATTCTTATTTTAACCAT
1 TTCCATATATAGAATTCTTATTGTAACCAT
*
41211329 TTCCATTTATAG
1 TTCCATATATAG
41211341 GATTGACGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (30 bp):
TTCCATATATAGAATTCTTATTGTAACCAT
Found at i:41215061 original size:2 final size:2
Alignment explanation
Indices: 41215054--41215081 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41215044 TTAGATTTCC
41215054 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
41215082 TCCACATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41215591 original size:50 final size:51
Alignment explanation
Indices: 41215525--41215621 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 51
41215515 TCCTCTTTCA
*
41215525 AGCCATACAACAGGAAGCTT-AAAAAGAGCTATTAATCAGAAAGCTCATAAG
1 AGCCATACAACAGGAAG-TTCAAAAAGAACTATTAATCAGAAAGCTCATAAG
* * * *
41215576 AGCCATA-ATCAGGAAGTTCACAAAGAACTTTTAATCAGGAAGCTCA
1 AGCCATACAACAGGAAGTTCAAAAAGAACTATTAATCAGAAAGCTCA
41215622 CGAAGGCCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
49 2 0.05
50 31 0.77
51 7 0.17
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.20
Consensus pattern (51 bp):
AGCCATACAACAGGAAGTTCAAAAAGAACTATTAATCAGAAAGCTCATAAG
Found at i:41215611 original size:26 final size:25
Alignment explanation
Indices: 41215535--41215644 Score: 82
Period size: 26 Copynumber: 4.4 Consensus size: 25
41215525 AGCCATACAA
* * *
41215535 CAGGAAGCTTAAAAAGAGCTATTAAT
1 CAGGAAGCTCACAAAGACCT-TTAAT
* * *
41215561 CAGAAAGCTCA-TAAGAGCC-ATAAT
1 CAGGAAGCTCACAAAGA-CCTTTAAT
* *
41215585 CAGGAAGTTCACAAAGAACTTTTAAT
1 CAGGAAGCTCACAAAG-ACCTTTAAT
* *
41215611 CAGGAAGCTCACGAAGGCCTTTAAT
1 CAGGAAGCTCACAAAGACCTTTAAT
41215636 CAGG-AGCTC
1 CAGGAAGCTC
41215645 CGGATAGCCA
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
24 18 0.27
25 19 0.29
26 29 0.44
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (25 bp):
CAGGAAGCTCACAAAGACCTTTAAT
Found at i:41217531 original size:68 final size:66
Alignment explanation
Indices: 41217392--41217531 Score: 185
Period size: 68 Copynumber: 2.1 Consensus size: 66
41217382 TTTTCAGATT
*
41217392 ATTTTCATTTTCATTTTGGAAAAACCATATTCATTTCCAAATGATTCCATTTCTCTATTTTCATT
1 ATTTTCATTTTCATTTTGGAAAAACCATATTCATTTCCAAATGATTCCATTTCTCCATTTTCA--
*
41217457 TTC
64 TCC
*
41217460 ATTTTCATTTTTATTTTGGAGAAAACCATAATT-ATTTCCAAATGATTTCTCATTTCTCCATTTT
1 ATTTTCATTTTCATTTTGGA-AAAACCAT-ATTCATTTCCAAATGA-TTC-CATTTCTCCATTTT
41217524 CA-CC
62 CATCC
41217528 ATTT
1 ATTT
41217532 CTATTCATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
68 24 0.37
69 20 0.31
70 6 0.09
71 15 0.23
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (66 bp):
ATTTTCATTTTCATTTTGGAAAAACCATATTCATTTCCAAATGATTCCATTTCTCCATTTTCATC
C
Found at i:41225698 original size:58 final size:53
Alignment explanation
Indices: 41225553--41225698 Score: 168
Period size: 54 Copynumber: 2.6 Consensus size: 53
41225543 TAGAAAAACC
* *
41225553 ATATTATCATATTTTAAAAGTAAATTAACCGATCGATCAATATTTAAAAGACAA
1 ATATTATCATATTTT-AAAGTAAATTGACCGGTCGATCAATATTTAAAAGACAA
* *
41225607 ATATTATCATATTTATAAAGTAAATTGATCGGTCAGA-CAATTTTTAAAAGACAAAA
1 ATATTATCATATTT-TAAAGTAAATTGACCGGTC-GATCAATATTTAAAAGAC--AA
*
41225663 TGATATTATCATATTTGTAAAGTAAATTGGCCGGTC
1 --ATATTATCATATTT-TAAAGTAAATTGACCGGTC
41225699 TTTTAAAGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
54 43 0.54
55 3 0.04
56 2 0.03
58 31 0.39
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (53 bp):
ATATTATCATATTTTAAAGTAAATTGACCGGTCGATCAATATTTAAAAGACAA
Found at i:41227908 original size:51 final size:52
Alignment explanation
Indices: 41227843--41227942 Score: 159
Period size: 51 Copynumber: 1.9 Consensus size: 52
41227833 ATACGTCGAG
*
41227843 TTTTAAAGATAAAATCATATTATCATATTTG-AA-AAGTAAATTGATCGATT
1 TTTTAAAGACAAAATCATATTATCATATTTGTAATAAGTAAATTGATCGATT
*
41227893 TTTTAAAAGACAAAATGATATTATCATATTTGTAATAAGTAAATTGATCG
1 TTTT-AAAGACAAAATCATATTATCATATTTGTAATAAGTAAATTGATCG
41227943 GTCGGTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 4 0.09
51 25 0.56
52 2 0.04
53 14 0.31
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (52 bp):
TTTTAAAGACAAAATCATATTATCATATTTGTAATAAGTAAATTGATCGATT
Found at i:41231140 original size:14 final size:14
Alignment explanation
Indices: 41231121--41231157 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
41231111 TCAAGCTACC
41231121 TCCACCTCCACCGA
1 TCCACCTCCACCGA
*
41231135 TCCACCTCCACCGG
1 TCCACCTCCACCGA
41231149 TCCACCTCC
1 TCCACCTCC
41231158 GGTCCTGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.16, C:0.59, G:0.08, T:0.16
Consensus pattern (14 bp):
TCCACCTCCACCGA
Found at i:41232019 original size:15 final size:15
Alignment explanation
Indices: 41231981--41232019 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41231971 CTTTTTAGAT
*
41231981 TTTAATTTAATTTAA
1 TTTAATTTTATTTAA
*
41231996 TTTAATTTTATTTTA
1 TTTAATTTTATTTAA
*
41232011 TTTCATTTT
1 TTTAATTTT
41232020 GTACAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTAATTTTATTTAA
Found at i:41232606 original size:25 final size:25
Alignment explanation
Indices: 41232572--41232624 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
41232562 TTTTTTTAAG
*
41232572 AATTGATTGTTTGTAATTAAATTCA
1 AATTAATTGTTTGTAATTAAATTCA
41232597 AATTAATTGTTTGTAATTAAATTCA
1 AATTAATTGTTTGTAATTAAATTCA
41232622 AAT
1 AAT
41232625 AAGTAATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (25 bp):
AATTAATTGTTTGTAATTAAATTCA
Found at i:41240664 original size:22 final size:23
Alignment explanation
Indices: 41240634--41240683 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
41240624 ACCTACTTTC
* *
41240634 TTACTGTAGTAATTTTCG-GGTA
1 TTACAGTAGTAATTTTCGAGATA
41240656 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
41240679 TTACA
1 TTACA
41240684 ACAAGTGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:41241246 original size:18 final size:18
Alignment explanation
Indices: 41241187--41241246 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
41241177 AATCACACAG
* *
41241187 TTGCGAGCTCATCCAAAG
1 TTGCGAACTCATCCAAAT
*
41241205 TTACGAACTCATCCAAAT
1 TTGCGAACTCATCCAAAT
*
41241223 TCGCGAACTCATCCAAAT
1 TTGCGAACTCATCCAAAT
41241241 TTGCGA
1 TTGCGA
41241247 GCTTAGCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (18 bp):
TTGCGAACTCATCCAAAT
Found at i:41253816 original size:19 final size:18
Alignment explanation
Indices: 41253794--41253832 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41253784 ATTACAAAAT
*
41253794 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
*
41253813 AATTCCAAATATTTATAA
1 AATTCAAAATATTTATAA
41253831 AA
1 AA
41253833 ATATCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:41253833 original size:19 final size:19
Alignment explanation
Indices: 41253811--41253848 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
41253801 AATAATTTTT
41253811 AAAAT-TCCAAATATTTATA
1 AAAATATCCAAAT-TTTATA
41253830 AAAATATCCAAATTTTATA
1 AAAATATCCAAATTTTATA
41253849 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATCCAAATTTTATA
Found at i:41255315 original size:22 final size:20
Alignment explanation
Indices: 41255279--41255337 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
41255269 GGCCCGACCC
41255279 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
41255301 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
41255322 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
41255338 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:41255339 original size:11 final size:11
Alignment explanation
Indices: 41255319--41255376 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
41255309 TAAAAATTAA
41255319 AAAAAGTATTTT
1 AAAAA-TATTTT
41255331 AAAAATATTTT
1 AAAAATATTTT
**
41255342 --AAA-ATTAA
1 AAAAATATTTT
41255350 AAAAATTATTTT
1 AAAAA-TATTTT
41255362 AAAAATATTTT
1 AAAAATATTTT
41255373 AAAA
1 AAAA
41255377 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 3 0.08
11 16 0.42
12 13 0.34
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:41255349 original size:31 final size:31
Alignment explanation
Indices: 41255304--41255383 Score: 142
Period size: 31 Copynumber: 2.5 Consensus size: 31
41255294 ACCAAAAATT
41255304 TATTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAGTATTTTAAAAA
*
41255336 TATTTTAAAATTAAAAAAATTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAGTATTTTAAAAA
41255367 TATTTTAAAATTAAAAA
1 TATTTTAAAATTAAAAA
41255384 TAAATATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 41 0.87
32 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
TATTTTAAAATTAAAAAAAGTATTTTAAAAA
Found at i:41262576 original size:10 final size:11
Alignment explanation
Indices: 41262558--41262584 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41262548 TCCATCAACC
41262558 ACAAAAAAAAA
1 ACAAAAAAAAA
41262569 ACAAAAAAAAA
1 ACAAAAAAAAA
41262580 ACAAA
1 ACAAA
41262585 TTCAAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:41269874 original size:19 final size:19
Alignment explanation
Indices: 41269850--41269887 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41269840 AATTATTTAT
41269850 TAAATT-TAATTAGAATATA
1 TAAATTATAATTA-AATATA
*
41269869 TAAATTATATTTAAATATA
1 TAAATTATAATTAAATATA
41269888 ATAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TAAATTATAATTAAATATA
Found at i:41271756 original size:72 final size:72
Alignment explanation
Indices: 41271665--41271836 Score: 231
Period size: 72 Copynumber: 2.4 Consensus size: 72
41271655 AAAATCACAT
* * *
41271665 ATAAACAACTATTGATAAAACTAATTTAGTA-AAAAATAAGTAGAACATAAATTCAATATCTAAA
1 ATAAACAACTATTAATAAAACTAATTTA-CACAAAAATAAGTAGAACATAAATTCAATATCCAAA
*
41271729 GACCAAAC
65 AACCAAAC
*
41271737 ATAAACAACTATTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTAATAAAACTA-ATTTACACAAAAATAAGTAGAACATAAATTCAATATCCAAA
41271801 AACCAAAC
65 AACCAAAC
* *
41271809 ATAAATAACTATTGATTAAAACATAATT
1 ATAAACAACTATT-AATAAAAC-TAATT
41271837 CGCTTATGCC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
71 1 0.01
72 75 0.85
73 9 0.10
74 3 0.03
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTAATAAAACTAATTTACACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:41272297 original size:18 final size:18
Alignment explanation
Indices: 41272276--41272341 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
41272266 TCCATCAATT
41272276 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
41272294 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
41272312 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
41272330 TGAACATCATTT
1 TGAACATCATTT
41272342 CTCATATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:41274927 original size:23 final size:23
Alignment explanation
Indices: 41274893--41274936 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
41274883 GAGGGTAGAG
41274893 GAACAAAGAACCAGCAGAGGGAA
1 GAACAAAGAACCAGCAGAGGGAA
*
41274916 GAACAAATAACCAGCAGAGGG
1 GAACAAAGAACCAGCAGAGGG
41274937 CAGAGATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.18, G:0.30, T:0.02
Consensus pattern (23 bp):
GAACAAAGAACCAGCAGAGGGAA
Found at i:41286408 original size:18 final size:19
Alignment explanation
Indices: 41286385--41286423 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41286375 TACAAATACA
*
41286385 AACATT-ACATAATTATTT
1 AACATTCACATAATAATTT
*
41286403 AACATTCACATCATAATTT
1 AACATTCACATAATAATTT
41286422 AA
1 AA
41286424 TCTTATCGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATAATTT
Found at i:41286965 original size:31 final size:31
Alignment explanation
Indices: 41286930--41286988 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
41286920 TTACAACATA
41286930 TTTCACATTCTATTTTCAATTCACTATCGTT
1 TTTCACATTCTATTTTCAATTCACTATCGTT
41286961 TTTCACATTCTATTTTCAATTCACTATC
1 TTTCACATTCTATTTTCAATTCACTATC
41286989 TCATATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTCACATTCTATTTTCAATTCACTATCGTT
Found at i:41287202 original size:218 final size:218
Alignment explanation
Indices: 41286824--41287263 Score: 826
Period size: 218 Copynumber: 2.0 Consensus size: 218
41286814 TGCTATATAT
*
41286824 AATAGTTTTCCACAATTTGTTCACATATCATTTAAACAATGGCACTATTCATTCCACGTTCAATT
1 AATAGTTTTCCACAATTTGTTCACATATCATTTAAACAATGGCACTATCCATTCCACGTTCAATT
41286889 CACGAGTATATAACTCGTGTATTCCATGTATTTACAACATATTTCACATTCTATTTTCAATTCAC
66 CACGAGTATATAACTCGTGTATTCCATGTATTTACAACATATTTCACATTCTATTTTCAATTCAC
41286954 TATCGTTTTTCACATTCTATTTTCAATTCACTATCTCATATTCTTAGCCCAAAGTAGATTTTATA
131 TATCGTTTTTCACATTCTATTTTCAATTCACTATCTCATATTCTTAGCCCAAAGTAGATTTTATA
* *
41287019 GAACATACCGGATATACGGAACA
196 AAACATACCGGATATACAGAACA
41287042 AATAGTTTTCCACAATTTGTTCACATATCATTTAAACAATGGCACTATCCATTCCACGTTCAATT
1 AATAGTTTTCCACAATTTGTTCACATATCATTTAAACAATGGCACTATCCATTCCACGTTCAATT
*
41287107 CATGAGTATATAACTCGTGTATTCCATGTATTTACAACATATTTCACATTCTATTTTCAATTCAC
66 CACGAGTATATAACTCGTGTATTCCATGTATTTACAACATATTTCACATTCTATTTTCAATTCAC
* *
41287172 TGTCGTTTTTCACATTCTATTTTCAATTCACTATCTCATATTCTTAGTCCAAAGTAGATTTTATA
131 TATCGTTTTTCACATTCTATTTTCAATTCACTATCTCATATTCTTAGCCCAAAGTAGATTTTATA
41287237 AAACATACCGGATATACAGAACA
196 AAACATACCGGATATACAGAACA
41287260 AATA
1 AATA
41287264 CAGAGGTGCA
Statistics
Matches: 216, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 216 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (218 bp):
AATAGTTTTCCACAATTTGTTCACATATCATTTAAACAATGGCACTATCCATTCCACGTTCAATT
CACGAGTATATAACTCGTGTATTCCATGTATTTACAACATATTTCACATTCTATTTTCAATTCAC
TATCGTTTTTCACATTCTATTTTCAATTCACTATCTCATATTCTTAGCCCAAAGTAGATTTTATA
AAACATACCGGATATACAGAACA
Found at i:41287323 original size:22 final size:22
Alignment explanation
Indices: 41287292--41287382 Score: 62
Period size: 22 Copynumber: 4.0 Consensus size: 22
41287282 CACTAATGAA
*
41287292 CAGAGGGCACTGAAGTGCT-AT
1 CAGAGAGCACTGAAGTGCTAAT
* * *
41287313 ACAGTGAGCACAGATGTGCTAAT
1 -CAGAGAGCACTGAAGTGCTAAT
*
41287336 CAGAGAGCACT-AACATGCTAATAAT
1 CAGAGAGCACTGAA-GTGC---TAAT
41287361 CAGAGAGCACT-AACGTGCTAAT
1 CAGAGAGCACTGAA-GTGCTAAT
41287383 AATCAGAGAG
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
21 1 0.02
22 31 0.56
23 2 0.04
25 21 0.38
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (22 bp):
CAGAGAGCACTGAAGTGCTAAT
Found at i:41287393 original size:27 final size:25
Alignment explanation
Indices: 41287332--41287392 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
41287322 ACAGATGTGC
41287332 TAATCAGAGAGCACTAACATGCTAA
1 TAATCAGAGAGCACTAACATGCTAA
*
41287357 TAATCAGAGAGCACTAACGTGCTAA
1 TAATCAGAGAGCACTAACATGCTAA
41287382 TAATCAGAGAG
1 TAATCAGAGAG
41287393 AGCGCTAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (25 bp):
TAATCAGAGAGCACTAACATGCTAA
Found at i:41290109 original size:15 final size:16
Alignment explanation
Indices: 41290089--41290118 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41290079 AAAATACTTT
41290089 ATTTAA-AATAAATAC
1 ATTTAATAATAAATAC
41290104 ATTTAATAATAAATA
1 ATTTAATAATAAATA
41290119 AAAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTTAATAATAAATAC
Found at i:41292251 original size:39 final size:41
Alignment explanation
Indices: 41292178--41292267 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 41
41292168 TAAAAAATAT
* ** *
41292178 TTATATTAAAAAACACTACCATAAATATGATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATACAATAAATATTGTA
*
41292219 TTATATTAAAAAATAC-A-AATAAATACAATAAATATTGTA
1 TTATATTAAAAAACACTACAATAAATACAATAAATATTGTA
*
41292258 TTGTATTAAA
1 TTATATTAAA
41292268 TATAAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 27 0.63
40 1 0.02
41 15 0.35
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATACAATAAATATTGTA
Found at i:41292412 original size:18 final size:18
Alignment explanation
Indices: 41292366--41292426 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
41292356 AGTTAGTGAT
*
41292366 TTAATATAA-ATATAAAA
1 TTAATATAATATATATAA
*
41292383 TTATCATTTAATATATATAA
1 TTA--ATATAATATATATAA
* *
41292403 TTAATATAATTTTTATAA
1 TTAATATAATATATATAA
41292421 TGTAAT
1 T-TAAT
41292427 GTATTGGACT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.09
18 13 0.37
19 9 0.26
20 10 0.29
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAATATAATATATATAA
Found at i:41299594 original size:19 final size:20
Alignment explanation
Indices: 41299560--41299602 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
41299550 GAAGTACTGT
41299560 TACTTTCCTTTAGGTATCGA
1 TACTTTCCTTTAGGTATCGA
* *
41299580 TACTTT-CTTTTGGTATTGA
1 TACTTTCCTTTAGGTATCGA
41299599 TACT
1 TACT
41299603 ATTTTTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (20 bp):
TACTTTCCTTTAGGTATCGA
Found at i:41301856 original size:34 final size:34
Alignment explanation
Indices: 41301818--41301885 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
41301808 AAATTACAAG
41301818 AAAATGACTTAATTTACTTACCAAATTGAATGAC
1 AAAATGACTTAATTTACTTACCAAATTGAATGAC
41301852 AAAATGACTTAATTTACTTACCAAATTGAATGAC
1 AAAATGACTTAATTTACTTACCAAATTGAATGAC
41301886 CTAATGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (34 bp):
AAAATGACTTAATTTACTTACCAAATTGAATGAC
Found at i:41302061 original size:19 final size:19
Alignment explanation
Indices: 41302021--41302061 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41302011 AATTAACTTA
*
41302021 TAATTAATCATAATTAGTT
1 TAATTAATCATAATTAGAT
41302040 TAATTAATCAATAATTA-AT
1 TAATTAATC-ATAATTAGAT
41302059 TAA
1 TAA
41302062 CATTAACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (19 bp):
TAATTAATCATAATTAGAT
Found at i:41310520 original size:19 final size:18
Alignment explanation
Indices: 41310498--41310548 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
41310488 GAAAATCACT
41310498 TAAAAATGTTAAAAAAAT-A
1 TAAAAATG--AAAAAAATAA
41310517 TAAAAATGAAAAAAATCAA
1 TAAAAATGAAAAAAAT-AA
41310536 TAAAAAT-AAAAAA
1 TAAAAATGAAAAAA
41310549 CTATAACGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.27
18 6 0.20
19 16 0.53
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
TAAAAATGAAAAAAATAA
Found at i:41310961 original size:18 final size:18
Alignment explanation
Indices: 41310938--41310974 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
41310928 TTTTTTTTGG
41310938 ATTTTTTTGAAAATTATA
1 ATTTTTTTGAAAATTATA
*
41310956 ATTTTTTTTAAAATTATA
1 ATTTTTTTGAAAATTATA
41310974 A
1 A
41310975 GTATTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTTTTTGAAAATTATA
Found at i:41311009 original size:20 final size:19
Alignment explanation
Indices: 41310981--41311021 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41310971 ATAAGTATTC
*
41310981 AAAACTTCAAACAAATTTTA
1 AAAAATTCAAA-AAATTTTA
*
41311001 AAAAATTCATAAAATTTTA
1 AAAAATTCAAAAAATTTTA
41311020 AA
1 AA
41311022 TACCTGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTCAAAAAATTTTA
Found at i:41311153 original size:20 final size:20
Alignment explanation
Indices: 41311111--41311156 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41311101 ATGTTTTGTA
* *
41311111 TTTTTATGAATTTTTGACAT
1 TTTTTAAGAAATTTTGACAT
*
41311131 TTTTTAAGAAATTTTGA-GT
1 TTTTTAAGAAATTTTGACAT
41311150 TTTTTAA
1 TTTTTAA
41311157 AGTAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (20 bp):
TTTTTAAGAAATTTTGACAT
Found at i:41318221 original size:24 final size:24
Alignment explanation
Indices: 41318189--41318236 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
41318179 TTTCCATCAG
41318189 TCTTAATTTAGGATCGTGTATGGC
1 TCTTAATTTAGGATCGTGTATGGC
41318213 TCTTAATTTAGGATCGTGTATGGC
1 TCTTAATTTAGGATCGTGTATGGC
41318237 AATAGACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (24 bp):
TCTTAATTTAGGATCGTGTATGGC
Found at i:41319510 original size:21 final size:21
Alignment explanation
Indices: 41319484--41319560 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
41319474 CAAAAAAAAT
41319484 AAAAAA-TCATTAAAATTATTA
1 AAAAAAGT-ATTAAAATTATTA
*
41319505 AAAAAAGTA-TAATAATGA-TA
1 AAAAAAGTATTAA-AATTATTA
* *
41319525 AAAAATATTTTTAAAATT-TTA
1 AAAAA-AGTATTAAAATTATTA
41319546 AAAAAAGTAATTAAA
1 AAAAAAGT-ATTAAA
41319561 TGCTGACCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 12 0.27
21 28 0.64
22 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (21 bp):
AAAAAAGTATTAAAATTATTA
Found at i:41320856 original size:13 final size:14
Alignment explanation
Indices: 41320838--41320867 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41320828 GGGTCGTTTA
41320838 TTTATTTA-TTGGT
1 TTTATTTATTTGGT
41320851 TTTATTTATTTGGT
1 TTTATTTATTTGGT
41320865 TTT
1 TTT
41320868 GGGCCCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (14 bp):
TTTATTTATTTGGT
Found at i:41326739 original size:25 final size:26
Alignment explanation
Indices: 41326682--41326742 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
41326672 TTTTTATCAG
*
41326682 GGTAAAATCGTCAAAATTTTACCGAA
1 GGTAAAATTGTCAAAATTTTACCGAA
**
41326708 GGT-AAATTGTCAAAATTTTATTG-A
1 GGTAAAATTGTCAAAATTTTACCGAA
41326732 GGTAAAATTGT
1 GGTAAAATTGT
41326743 GGTGAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 24 0.77
26 3 0.10
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (26 bp):
GGTAAAATTGTCAAAATTTTACCGAA
Found at i:41332538 original size:58 final size:59
Alignment explanation
Indices: 41332448--41332565 Score: 220
Period size: 58 Copynumber: 2.0 Consensus size: 59
41332438 TAAAGCATAC
41332448 AATGAGTTGACACAAGAATTGAACAAGCCATGAATCTGAAGGTCA-GCAAAGCTCACTA
1 AATGAGTTGACACAAGAATTGAACAAGCCATGAATCTGAAGGTCAGGCAAAGCTCACTA
*
41332506 AATGAGTTGACACAAGAATTGAACAAGCCATGAATCTGACGGTCAGGCAAAGCTCACTA
1 AATGAGTTGACACAAGAATTGAACAAGCCATGAATCTGAAGGTCAGGCAAAGCTCACTA
41332565 A
1 A
41332566 TGCCGTGTCA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 44 0.76
59 14 0.24
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (59 bp):
AATGAGTTGACACAAGAATTGAACAAGCCATGAATCTGAAGGTCAGGCAAAGCTCACTA
Found at i:41349489 original size:24 final size:25
Alignment explanation
Indices: 41349449--41349497 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
41349439 TCCTCTCTCC
41349449 AACTTTCTCTCTCCTTC-TTCGTTT
1 AACTTTCTCTCTCCTTCTTTCGTTT
*
41349473 AACTCTTCT-TCTTCTTCTTTCGTTT
1 AACT-TTCTCTCTCCTTCTTTCGTTT
41349498 GTTGGTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.08, C:0.31, G:0.04, T:0.57
Consensus pattern (25 bp):
AACTTTCTCTCTCCTTCTTTCGTTT
Found at i:41355946 original size:31 final size:31
Alignment explanation
Indices: 41355908--41355971 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
41355898 TTTTCTACGG
41355908 ATGACAAGATTCGAACAAGACTGAATAGGGT
1 ATGACAAGATTCGAACAAGACTGAATAGGGT
41355939 ATGACAAGATTCGAACAAGACTGAATAGGGT
1 ATGACAAGATTCGAACAAGACTGAATAGGGT
41355970 AT
1 AT
41355972 TCTCCTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.20
Consensus pattern (31 bp):
ATGACAAGATTCGAACAAGACTGAATAGGGT
Found at i:41356419 original size:2 final size:2
Alignment explanation
Indices: 41356412--41356458 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
41356402 TTATTGGCTG
41356412 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
41356454 AT AT A
1 AT AT A
41356459 GATCAAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41356485 original size:19 final size:22
Alignment explanation
Indices: 41356452--41356491 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
41356442 ATATATATAT
41356452 ATATATAGATCAAAA-TAAATC
1 ATATATAGATCAAAACTAAATC
41356473 ATATATA-AT-AAAACTAAAT
1 ATATATAGATCAAAACTAAAT
41356492 TAAAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (22 bp):
ATATATAGATCAAAACTAAATC
Found at i:41356885 original size:37 final size:37
Alignment explanation
Indices: 41356842--41356930 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
41356832 ATCATAAATA
*
41356842 AATAAACTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
* *
41356879 ATTAAACTAATTAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
41356916 AATGAACTAATCAAT
1 AATAAACTAATCAAT
41356931 ATATTTATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:41357010 original size:33 final size:33
Alignment explanation
Indices: 41356973--41357048 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
41356963 TTAAAACTTG
*
41356973 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
41357006 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
41357039 AATTATACAT
1 AATTATACAT
41357049 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:41359010 original size:50 final size:50
Alignment explanation
Indices: 41358895--41359143 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
41358885 GATAATAACA
* * ** * *
41358895 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
41358946 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
41358996 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
41359046 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* * *
41359101 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
41359144 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.20
53 4 0.02
54 1 0.01
55 2 0.01
56 37 0.22
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:41359081 original size:100 final size:104
Alignment explanation
Indices: 41358894--41359143 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 104
41358884 TGATAATAAC
** * *
41358894 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
41358959 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* *
41358996 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
41359060 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
** *
41359101 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41359144 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.28
103 4 0.03
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:41366806 original size:50 final size:50
Alignment explanation
Indices: 41366691--41366939 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
41366681 GATAATAACA
* * ** * *
41366691 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
41366742 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
41366792 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
41366842 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
41366897 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
41366940 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:41366877 original size:100 final size:104
Alignment explanation
Indices: 41366690--41366939 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
41366680 TGATAATAAC
** * *
41366690 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
41366755 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* *
41366792 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
41366856 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
41366897 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41366940 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:41367311 original size:30 final size:30
Alignment explanation
Indices: 41367277--41367334 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41367267 CCTTGACTCT
*
41367277 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
41367307 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
41367335 AAGGCTCGGA
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:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:41372400 original size:46 final size:46
Alignment explanation
Indices: 41372316--41372452 Score: 154
Period size: 52 Copynumber: 2.8 Consensus size: 46
41372306 TTTGAGTACT
* *
41372316 TCTGATCAAGTGACAAAGT-GATAAGTGGT-AGCT-TTAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TGATAGCTACACTTA
41372362 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATA------GCTACACTTA
41372414 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCT
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCT
41372453 TCGGCTACAC
Statistics
Matches: 80, Mismatches: 2, Indels: 18
0.80 0.02 0.18
Matches are distributed among these distances:
45 11 0.14
46 23 0.29
52 46 0.57
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTACACTTA
Found at i:41372401 original size:52 final size:52
Alignment explanation
Indices: 41372330--41372481 Score: 268
Period size: 52 Copynumber: 2.9 Consensus size: 52
41372320 ATCAAGTGAC
* **
41372330 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
41372382 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
41372434 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
41372482 AGTGATAAGT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 96 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:41372499 original size:37 final size:37
Alignment explanation
Indices: 41372455--41372601 Score: 244
Period size: 37 Copynumber: 4.0 Consensus size: 37
41372445 TGATAGCTTC
*
41372455 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
41372492 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
41372529 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
41372566 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
41372601 G
1 G
41372602 ATCATACGTA
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
35 11 0.10
36 4 0.04
37 90 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:41375084 original size:26 final size:26
Alignment explanation
Indices: 41375055--41375114 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
41375045 AACACTCAAA
41375055 TTTTAAACTA-AACTTTTCAAAAGCAC
1 TTTTAAAC-AGAACTTTTCAAAAGCAC
** *
41375081 TTTTTCACAGCACTTTTCAAAAGCAC
1 TTTTAAACAGAACTTTTCAAAAGCAC
41375107 TTTCTAAA
1 TTT-TAAA
41375115 AGCAATGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
25 1 0.04
26 24 0.89
27 2 0.07
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (26 bp):
TTTTAAACAGAACTTTTCAAAAGCAC
Found at i:41375110 original size:12 final size:13
Alignment explanation
Indices: 41375066--41375118 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
41375056 TTTAAACTAA
41375066 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
41375079 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
41375092 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
41375105 AC-TTTCTAAAAGC
1 ACTTTTC-AAAAGC
41375118 A
1 A
41375119 ATGAAGAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 9 0.26
13 21 0.60
14 5 0.14
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41375118 original size:26 final size:26
Alignment explanation
Indices: 41375066--41375118 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
41375056 TTTAAACTAA
* * *
41375066 ACTTTTCAAAAGCACTTTTTCACAGC
1 ACTTTTCAAAAGCACTTTCTAAAAGC
41375092 ACTTTTCAAAAGCACTTTCTAAAAGC
1 ACTTTTCAAAAGCACTTTCTAAAAGC
41375118 A
1 A
41375119 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTTCTAAAAGC
Found at i:41381880 original size:12 final size:11
Alignment explanation
Indices: 41381859--41381893 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
41381849 TTGAACCAAA
41381859 TTTTTATAATT
1 TTTTTATAATT
41381870 TTTTTAGTAATT
1 TTTTTA-TAATT
*
41381882 TTTTAATAATT
1 TTTTTATAATT
41381893 T
1 T
41381894 ATTCAATCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:41385155 original size:19 final size:19
Alignment explanation
Indices: 41385131--41385167 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41385121 TTACTTATTT
41385131 TTTTTAACTTAATTAATAA
1 TTTTTAACTTAATTAATAA
*
41385150 TTTTTAATTTAATTAATA
1 TTTTTAACTTAATTAATA
41385168 TACCTCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAACTTAATTAATAA
Found at i:41387214 original size:31 final size:31
Alignment explanation
Indices: 41387174--41387252 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
41387164 CATTTTATTG
* * *
41387174 ATAATCAAATATATGTACTCTTCGAA-TGCAT
1 ATAACCAAATATATGTACTCATC-AAGAGCAT
* * *
41387205 ATAACCAAATATTTATATTCATCAAGAGCAT
1 ATAACCAAATATATGTACTCATCAAGAGCAT
*
41387236 ATAACCAAATGTATGTA
1 ATAACCAAATATATGTA
41387253 TATATTCCAC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (31 bp):
ATAACCAAATATATGTACTCATCAAGAGCAT
Found at i:41387305 original size:2 final size:2
Alignment explanation
Indices: 41387298--41387355 Score: 98
Period size: 2 Copynumber: 28.5 Consensus size: 2
41387288 CACATCAACG
*
41387298 TA TA TA TA CTA TA GA 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
41387341 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
41387356 TTATCAAACA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:41399303 original size:21 final size:21
Alignment explanation
Indices: 41399277--41399320 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41399267 TGCAAAGAAG
41399277 TGCTTTTAAAAAGTTTAGTAT
1 TGCTTTTAAAAAGTTTAGTAT
* **
41399298 TGCTTTTGAAGTGTTTAGTAT
1 TGCTTTTAAAAAGTTTAGTAT
41399319 TG
1 TG
41399321 TTGTCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (21 bp):
TGCTTTTAAAAAGTTTAGTAT
Found at i:41406673 original size:17 final size:18
Alignment explanation
Indices: 41406628--41406675 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
41406618 AAATAAATAG
*
41406628 TATTTTTAT-TTTTATAA
1 TATTTTTATAATTTATAA
**
41406645 TATTTTGGTAATTTAT-A
1 TATTTTTATAATTTATAA
41406662 TATTTTTATAATTT
1 TATTTTTATAATTT
41406676 TCTAAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TATTTTTATAATTTATAA
Found at i:41414750 original size:19 final size:18
Alignment explanation
Indices: 41414726--41414768 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
41414716 TTTCATGTAA
* *
41414726 AATTTTGGGATGACTCTTG
1 AATTTTAGGATGACAC-TG
*
41414745 AATTTTAGGATTACACTG
1 AATTTTAGGATGACACTG
41414763 AATTTT
1 AATTTT
41414769 CATTTTATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (18 bp):
AATTTTAGGATGACACTG
Found at i:41415850 original size:17 final size:17
Alignment explanation
Indices: 41415828--41415861 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41415818 ACAATTAAGA
*
41415828 TAATATTTTTACATTAT
1 TAATATTATTACATTAT
*
41415845 TAATATTATTATATTAT
1 TAATATTATTACATTAT
41415862 ATTTTGGTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATATTATTACATTAT
Found at i:41425733 original size:19 final size:20
Alignment explanation
Indices: 41425694--41425733 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41425684 TCTTTAACAA
* *
41425694 TATATATTTTTATTTTTATT
1 TATATATTTTTATTATGATT
41425714 TATA-ATTTTTATTATGATT
1 TATATATTTTTATTATGATT
41425733 T
1 T
41425734 GAAACTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TATATATTTTTATTATGATT
Found at i:41426315 original size:13 final size:13
Alignment explanation
Indices: 41426297--41426321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41426287 CTTGAGAACT
41426297 CAAACAACAAAAC
1 CAAACAACAAAAC
41426310 CAAACAACAAAA
1 CAAACAACAAAA
41426322 AGTTTCTCTC
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:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAACAACAAAAC
Found at i:41427280 original size:20 final size:20
Alignment explanation
Indices: 41427252--41427291 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41427242 TTTTAGATTG
*
41427252 TAAAAAATTATTATAATTTT
1 TAAAAAATTATTACAATTTT
* *
41427272 TAAATAATTTTTACAATTTT
1 TAAAAAATTATTACAATTTT
41427292 ATTCATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAAAATTATTACAATTTT
Found at i:41443127 original size:7 final size:7
Alignment explanation
Indices: 41443117--41443141 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41443107 TGCACATTGC
41443117 TCAGCAT
1 TCAGCAT
41443124 TCAGCAT
1 TCAGCAT
41443131 TCAGCAT
1 TCAGCAT
41443138 TCAG
1 TCAG
41443142 GATCCAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (7 bp):
TCAGCAT
Found at i:41445813 original size:22 final size:24
Alignment explanation
Indices: 41445782--41445854 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 24
41445772 CGGCCCGAAT
41445782 TATATATTAAAAATATATATTTT-
1 TATATATTAAAAATATATATTTTA
*
41445805 TAT-TTTTAATCAAATATATATTTTA
1 TATATATTAA--AAATATATATTTTA
*
41445830 TATATATT--AAATATATATTTAA
1 TATATATTAAAAATATATATTTTA
41445852 TAT
1 TAT
41445855 GGGCCGGGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
22 21 0.49
23 3 0.07
24 13 0.30
25 3 0.07
26 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATATTAAAAATATATATTTTA
Found at i:41445834 original size:11 final size:11
Alignment explanation
Indices: 41445817--41445854 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
41445807 TTTTTAATCA
41445817 AATATATATTT
1 AATATATATTT
* *
41445828 TATATATATTA
1 AATATATATTT
41445839 AATATATATTT
1 AATATATATTT
41445850 AATAT
1 AATAT
41445855 GGGCCGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:41446498 original size:25 final size:24
Alignment explanation
Indices: 41446444--41446501 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
41446434 TACACTAAGA
*
41446444 TAATGAAATTTATTATATAATATAT
1 TAAT-AAATTTATTACATAATATAT
*
41446469 AAATAAATTTATTTACATAATA-ATT
1 TAATAAATTTA-TTACATAATATA-T
41446494 TAATAAAT
1 TAATAAAT
41446502 ATGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TAATAAATTTATTACATAATATAT
Found at i:41451068 original size:22 final size:24
Alignment explanation
Indices: 41451026--41451069 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41451016 TTAATATAAA
41451026 TTTAATATGTTATGATAAAACTAT
1 TTTAATATGTTATGATAAAACTAT
*
41451050 TTTAAT-TTTTAT-ATAAAACT
1 TTTAATATGTTATGATAAAACT
41451070 TAAAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (24 bp):
TTTAATATGTTATGATAAAACTAT
Found at i:41453511 original size:28 final size:27
Alignment explanation
Indices: 41453479--41453539 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
41453469 TTAAAATTTT
*
41453479 AATTAAGCT-TTAATAAAAAATTGTAATA
1 AATTAAGCTATTAATAAAAAAGT-TAA-A
* *
41453507 AATTAAGTTATTAATCAAAAAGTTAAA
1 AATTAAGCTATTAATAAAAAAGTTAAA
41453534 AATTAA
1 AATTAA
41453540 TTAAGTCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 11 0.38
29 11 0.38
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (27 bp):
AATTAAGCTATTAATAAAAAAGTTAAA
Found at i:41458975 original size:28 final size:27
Alignment explanation
Indices: 41458944--41458999 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
41458934 TCAAAGTTAC
41458944 TTTTACTATT-TTAAATATAAAATATAAT
1 TTTTAC-ATTATTAAATATAAAAT-TAAT
*
41458972 TTTTACATTATTAAATATTAAATTAAT
1 TTTTACATTATTAAATATAAAATTAAT
41458999 T
1 T
41459000 ATAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTACATTATTAAATATAAAATTAAT
Found at i:41467683 original size:2 final size:2
Alignment explanation
Indices: 41467678--41467725 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
41467668 TTATATATGC
41467678 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
41467720 AT AT AT
1 AT AT AT
41467726 CACTATGTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41486490 original size:22 final size:23
Alignment explanation
Indices: 41486462--41486509 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
41486452 GAATGGAAAA
41486462 AAAAGAA-A-AAAAAAAGAAAGTT
1 AAAAGAACATAAAAAAA-AAAGTT
*
41486484 AAAAGAACATAAAAAAAAAATTT
1 AAAAGAACATAAAAAAAAAAGTT
41486507 AAA
1 AAA
41486510 TTGCTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 9 0.39
24 7 0.30
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.12
Consensus pattern (23 bp):
AAAAGAACATAAAAAAAAAAGTT
Found at i:41487229 original size:38 final size:37
Alignment explanation
Indices: 41487119--41487219 Score: 111
Period size: 38 Copynumber: 2.8 Consensus size: 37
41487109 GAATTTCTTG
* * * *
41487119 TTTTGAAAACACGAGAA-TTTCAAGACATAATATTTT
1 TTTTGAAAACACGAAAATTTTCAAAACACAAGATTTT
*
41487155 TTTT-AAAA-ACGAAAATTTAT-GAAACACAAGATTTTT
1 TTTTGAAAACACGAAAATTT-TCAAAACACAAGA-TTTT
41487191 TTTTGAAAACACGAAAATTTTCAAAACAC
1 TTTTGAAAACACGAAAATTTTCAAAACAC
41487220 CGAAATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
34 6 0.11
35 13 0.25
36 13 0.25
37 5 0.09
38 16 0.30
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.34
Consensus pattern (37 bp):
TTTTGAAAACACGAAAATTTTCAAAACACAAGATTTT
Found at i:41487246 original size:17 final size:17
Alignment explanation
Indices: 41487190--41487251 Score: 79
Period size: 18 Copynumber: 3.5 Consensus size: 17
41487180 ACAAGATTTT
41487190 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
* *
41487207 ATTTTCAAAACACCGAAA
1 TTTTTGAAAACA-CGAAA
*
41487225 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGA-AA
41487243 TTTTTGAAA
1 TTTTTGAAA
41487252 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
17 13 0.34
18 25 0.66
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:41487422 original size:18 final size:19
Alignment explanation
Indices: 41487378--41487442 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
41487368 AACACGAAGT
* *
41487378 AATTTTTTAGAAAACATGTAA
1 AATTTTTT-GAAAACACG-GA
*
41487399 AATTTTTTG-AAACACGGG
1 AATTTTTTGAAAACACGGA
*
41487417 AA-TTTTTGAAAACACGTA
1 AATTTTTTGAAAACACGGA
41487435 AATTTTTT
1 AATTTTTT
41487443 TATTTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 6 0.16
18 11 0.30
19 11 0.30
20 1 0.03
21 8 0.22
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (19 bp):
AATTTTTTGAAAACACGGA
Found at i:41487573 original size:22 final size:21
Alignment explanation
Indices: 41487546--41487588 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
41487536 CGTTACCTTA
41487546 TTTTTGAAAACACGAGAAATTT
1 TTTTTGAAAACACGA-AAATTT
*
41487568 TTTTTGAAGACACGAAAATTT
1 TTTTTGAAAACACGAAAATTT
41487589 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (21 bp):
TTTTTGAAAACACGAAAATTT
Done.