Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 181 of 240
Found at i:55821585 original size:30 final size:27
Alignment explanation
Indices: 55821529--55821610 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 27
55821519 AGATAAACTC
55821529 ACCGGCAGAGGGCAGAG-GAACAAAGA
1 ACCGGCAGAGGGCAGAGAGAACAAAGA
*
55821555 ACCGGCAGAGGGCAGAGATGAGGGCAAAGA
1 ACCGGCAGAGGGCAGAGA-GA--ACAAAGA
*
55821585 ACCAGCAGAGGGCAGAGAG--CAAAGA
1 ACCGGCAGAGGGCAGAGAGAACAAAGA
55821610 A
1 A
55821611 AGGCGTTCGT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
25 7 0.14
26 17 0.34
28 2 0.04
29 1 0.02
30 23 0.46
ACGTcount: A:0.41, C:0.18, G:0.39, T:0.01
Consensus pattern (27 bp):
ACCGGCAGAGGGCAGAGAGAACAAAGA
Found at i:55823453 original size:111 final size:111
Alignment explanation
Indices: 55823317--55823541 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 111
55823307 CGAGTTTTTG
55823317 AATCTCATTTTATTATCCTAACTTTATTTGAAGTTTTCTCGAATCGAGTCGAGTGAGATGGAATT
1 AATCTCATTTTATTATCCTAACTTTATTTGAAGTTTTCTCGAATCGAGTCGAGTGAGATGGAATT
*
55823382 CGAATCGAATCGATTCGAATATATTTGTTCGAGTTAAATTTTAAAA
66 CGAATCGAATCGAATCGAATATATTTGTTCGAGTTAAATTTTAAAA
55823428 AATCTCATTTTATTATCCTAACTTTATTTGAAGTTTTCTCGAATCGAGTCGAGTGAGATGGAATT
1 AATCTCATTTTATTATCCTAACTTTATTTGAAGTTTTCTCGAATCGAGTCGAGTGAGATGGAATT
55823493 CGAATCGAATCGAATCGAATATATTTGTTCGAGTTAAATTTTAAAA
66 CGAATCGAATCGAATCGAATATATTTGTTCGAGTTAAATTTTAAAA
55823539 AAT
1 AAT
55823542 AATTTTGGGT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (111 bp):
AATCTCATTTTATTATCCTAACTTTATTTGAAGTTTTCTCGAATCGAGTCGAGTGAGATGGAATT
CGAATCGAATCGAATCGAATATATTTGTTCGAGTTAAATTTTAAAA
Found at i:55824439 original size:9 final size:9
Alignment explanation
Indices: 55824425--55824461 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55824415 TATAGTTTGA
55824425 TATTCGAAT
1 TATTCGAAT
55824434 TATTCGAAT
1 TATTCGAAT
*
55824443 TATTCGAGT
1 TATTCGAAT
55824452 TATTCGAAT
1 TATTCGAAT
55824461 T
1 T
55824462 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55824532 original size:9 final size:9
Alignment explanation
Indices: 55824515--55824545 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55824505 TCGAGTTGAT
55824515 TCGAATAAC
1 TCGAATAAC
*
55824524 TCGATTAAC
1 TCGAATAAC
55824533 TCGAATAAC
1 TCGAATAAC
55824542 TCGA
1 TCGA
55824546 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:55832472 original size:45 final size:44
Alignment explanation
Indices: 55832375--55832480 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 44
55832365 TACCCCACAG
* * * * *
55832375 ATGAAATCTGTCTTTGGCTGTGGATGCACAAAAATATCTCGTGA
1 ATGAAATTTGCCTCTGGTTGTGGATGCACAAAAATATCCCGTGA
* *
55832419 ATGAAATTTTCCTCTGGTTGTGGTTGCACAAAAAATATCCCGT-A
1 ATGAAATTTGCCTCTGGTTGTGGATGCAC-AAAAATATCCCGTGA
*
55832463 GATGGAATTTGCCTCTGG
1 -ATGAAATTTGCCTCTGG
55832481 CAGTGGATAC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
44 24 0.47
45 27 0.53
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (44 bp):
ATGAAATTTGCCTCTGGTTGTGGATGCACAAAAATATCCCGTGA
Found at i:55849471 original size:44 final size:44
Alignment explanation
Indices: 55849421--55850030 Score: 700
Period size: 44 Copynumber: 13.9 Consensus size: 44
55849411 ATCTACTTCG
* *
55849421 AATCTTCCACCTATTCCGCTGCTGGCCAGGGAGATAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* ** * * *
55849465 AATCTTCCACCTATTCCGCTGCTAATAAGAGAGATAGGACATAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * * **
55849509 AATCTTCAACATATTCCACTGCTGTTCAGGGATCTAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * * *
55849553 GATCTTCCACCTATTCCACTGCTGTTCAAGGAGCTAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * *
55849597 TATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGGCTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * * * *
55849641 AATCTTCCACCTACTCCGCTGCTGATTAGGGGGATAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * * *
55849685 AATCTTTCACCTATTCCGCTGCTGTTCAGGGAGCTAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * * *
55849729 AATCTTCAACCTACTCCGCTGCTGGTCAGGGGGATAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * * * * *
55849773 AATCTTTCACATATTTCGCTGCTGTTCAGGGAGCTAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* *
55849817 AATCTTCAACCTATTCCACTACTGGTCAGGGAGATATGG-CTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATA-GGACTTAC
* * * *
55849861 AATCTTCCACCTACTCCACTACTGGTTAGGGGGATAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * *
55849905 AATCTTTCACCTACTCCACTGCTGGTCAGGGGGATAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* * * * * *
55849949 AATCTTTCACCTATTCCGCTACTGTTTAGGGAGCTAGGACTTAC
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
* *
55849993 AATCTTCAATCTATTCCACTGCTGGTCAGGGAGATAGG
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGG
55850031 GCTTTGTGAT
Statistics
Matches: 479, Mismatches: 85, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
43 2 0.00
44 475 0.99
45 2 0.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTAC
Found at i:55855756 original size:6 final size:6
Alignment explanation
Indices: 55855747--55855771 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55855737 TTTATTTTAT
55855747 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
55855772 AAATTTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:55855793 original size:21 final size:21
Alignment explanation
Indices: 55855763--55855802 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55855753 TTAATATTAA
55855763 TATTAATATAAATTTTAAATT
1 TATTAATATAAATTTTAAATT
* **
55855784 TATTATTATATTTTTTAAA
1 TATTAATATAAATTTTAAA
55855803 AATATTTATG
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:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATATAAATTTTAAATT
Found at i:55855808 original size:21 final size:21
Alignment explanation
Indices: 55855761--55855808 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
55855751 TATTAATATT
55855761 AATATTAATATAAATTTTAAA
1 AATATTAATATAAATTTTAAA
** * **
55855782 TTTATTATTATATTTTTTAAA
1 AATATTAATATAAATTTTAAA
55855803 AATATT
1 AATATT
55855809 TATGTATTTT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTAATATAAATTTTAAA
Found at i:55862960 original size:17 final size:17
Alignment explanation
Indices: 55862935--55862968 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55862925 ATTATTTTAA
*
55862935 AATTAAATTAATTAATT
1 AATTAAATTAAATAATT
*
55862952 AATTCAATTAAATAATT
1 AATTAAATTAAATAATT
55862969 CACACAACCC
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:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAAATTAAATAATT
Found at i:55870230 original size:30 final size:30
Alignment explanation
Indices: 55870196--55870263 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
55870186 AGATAAAATA
55870196 AAATTGGAAAAGTTACAGCTTATAAGAGTC
1 AAATTGGAAAAGTTACAGCTTATAAGAGTC
55870226 AAATTGGAAAAGTTACAGCTTATAAGAGTC
1 AAATTGGAAAAGTTACAGCTTATAAGAGTC
55870256 AAATTGGA
1 AAATTGGA
55870264 GATTCTTGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (30 bp):
AAATTGGAAAAGTTACAGCTTATAAGAGTC
Found at i:55871692 original size:6 final size:6
Alignment explanation
Indices: 55871683--55871710 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55871673 ACAAAAGAAA
55871683 ATGGGC ATGGGC ATGGGC ATGGGC ATGG
1 ATGGGC ATGGGC ATGGGC ATGGGC ATGG
55871711 TAAATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.50, T:0.18
Consensus pattern (6 bp):
ATGGGC
Found at i:55872113 original size:120 final size:120
Alignment explanation
Indices: 55871970--55872266 Score: 576
Period size: 120 Copynumber: 2.5 Consensus size: 120
55871960 TAATAAATGG
55871970 TAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
55872035 TTTTACAGTACCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTACCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
55872090 TAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
*
55872155 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTACCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
*
55872210 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
55872267 TAAATATGAT
Statistics
Matches: 175, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 175 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
TAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
TTTTACAGTACCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
Found at i:55872243 original size:18 final size:17
Alignment explanation
Indices: 55872215--55872249 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55872205 ATTATTAAGA
*
55872215 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55872232 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55872250 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55872479 original size:44 final size:45
Alignment explanation
Indices: 55872414--55872504 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
55872404 ACCTCTATTC
* * *
55872414 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
55872458 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
55872503 CA
1 CA
55872505 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:55872506 original size:16 final size:16
Alignment explanation
Indices: 55872485--55872553 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
55872475 GATTAGCTAT
55872485 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
55872501 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
55872518 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
55872534 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
55872550 TACA
1 TACA
55872554 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:55872527 original size:33 final size:32
Alignment explanation
Indices: 55872485--55872553 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
55872475 GATTAGCTAT
55872485 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
55872518 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
55872550 TACA
1 TACA
55872554 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:55873502 original size:219 final size:219
Alignment explanation
Indices: 55873116--55873558 Score: 780
Period size: 219 Copynumber: 2.0 Consensus size: 219
55873106 CCAGGTTGAC
*
55873116 AAAGGTTGAAAATATACCTTAAAAAAATCTAGTAAGAGCTAACCAATTATATTATGAAGCCTCTA
1 AAAGGTTGAAAATATACCTTAAAAAAATCTAATAAGAGCTAACCAATTATATTATGAAGCCTCTA
55873181 TCTAAATCACAAACCACGGTCGCAACAAATCGCCCTAGCCTATACTTGATCCACCCAAAAGAAAA
66 TCTAAATCACAAACCACGGTCGCAACAAATCGCCCTAGCCTATACTTGATCCACCCAAAAGAAAA
*
55873246 ATGAATAGAATAACTCTTCAAACTTTTCAAAGAGGAAAAGAAAACCC-TTTATGTTAGTCAAATA
131 ACGAATAGAATAACTCTTCAAACTTTTCAAAGAGGAAAAGAAAACCCTTTTATGTTAGTCAAATA
55873310 ATGATATTTAGGTAACCACTGAAA
196 ATGATATTTAGGTAACCACTGAAA
*
55873334 AAAGGTTGGAAAATATACCTTAAAAAAATCTAATAAGAGCTAACCAATTGTATTATGAAGCCTCT
1 AAAGGTT-GAAAATATACCTTAAAAAAATCTAATAAGAGCTAACCAATTATATTATGAAGCCTCT
* * * *
55873399 ATCTAAATCACAAACCACGGTGGCAACAAATCGCCCTAGGCTTTACTTGATCCACCCGAAAGAAA
65 ATCTAAATCACAAACCACGGTCGCAACAAATCGCCCTAGCCTATACTTGATCCACCCAAAAGAAA
* *
55873464 AACGAATAGAATAACTCTTCAAACTTTTCAAAGAGGAAAATAAAACCCTTTTCTGTTAGTCAAAT
130 AACGAATAGAATAACTCTTCAAACTTTTCAAAGAGGAAAAGAAAACCCTTTTATGTTAGTCAAAT
*
55873529 AATGATCTTTAGGTAACCACTGAAA
195 AATGATATTTAGGTAACCACTGAAA
55873554 AAAGG
1 AAAGG
55873559 ATAATATCTT
Statistics
Matches: 213, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
218 7 0.03
219 162 0.76
220 44 0.21
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (219 bp):
AAAGGTTGAAAATATACCTTAAAAAAATCTAATAAGAGCTAACCAATTATATTATGAAGCCTCTA
TCTAAATCACAAACCACGGTCGCAACAAATCGCCCTAGCCTATACTTGATCCACCCAAAAGAAAA
ACGAATAGAATAACTCTTCAAACTTTTCAAAGAGGAAAAGAAAACCCTTTTATGTTAGTCAAATA
ATGATATTTAGGTAACCACTGAAA
Found at i:55875941 original size:21 final size:21
Alignment explanation
Indices: 55875917--55875959 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55875907 TGAAATGAGA
*
55875917 AGTGAATTCTTTGATGGATTC
1 AGTGAATGCTTTGATGGATTC
55875938 AGTGAATGCTTTGATGGATTC
1 AGTGAATGCTTTGATGGATTC
55875959 A
1 A
55875960 ACTTGTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (21 bp):
AGTGAATGCTTTGATGGATTC
Found at i:55877881 original size:7 final size:7
Alignment explanation
Indices: 55877869--55877896 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
55877859 TAATTTTAGG
55877869 TTGTGAC
1 TTGTGAC
55877876 TTGTGAC
1 TTGTGAC
55877883 TTGTGAC
1 TTGTGAC
55877890 TTGTGAC
1 TTGTGAC
55877897 ATATTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (7 bp):
TTGTGAC
Found at i:55880332 original size:18 final size:18
Alignment explanation
Indices: 55880292--55880332 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
55880282 ACATTATAGA
*
55880292 ATAAATTTTAAAAATAAT
1 ATAAATTATAAAAATAAT
* *
55880310 TTAAATTATAAAAATTAT
1 ATAAATTATAAAAATAAT
55880328 ATAAA
1 ATAAA
55880333 ACCTTTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAATTATAAAAATAAT
Found at i:55880372 original size:26 final size:27
Alignment explanation
Indices: 55880318--55880372 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
55880308 ATTTAAATTA
55880318 TAAAAATTATATAAAACCTTTTAATAAT
1 TAAAAATTATATAAAA-CTTTTAATAAT
* * *
55880346 TAAAAATTATTTTAAA-TTTTTATAAT
1 TAAAAATTATATAAAACTTTTAATAAT
55880372 T
1 T
55880373 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.42
28 14 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAAATTATATAAAACTTTTAATAAT
Found at i:55880402 original size:21 final size:21
Alignment explanation
Indices: 55880376--55880415 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55880366 TATAATTTTT
55880376 TTAAAAAGTTAAAACAAAAAA
1 TTAAAAAGTTAAAACAAAAAA
**
55880397 TTAAAACTTTAAAACAAAA
1 TTAAAAAGTTAAAACAAAA
55880416 TATTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.23
Consensus pattern (21 bp):
TTAAAAAGTTAAAACAAAAAA
Found at i:55880445 original size:12 final size:11
Alignment explanation
Indices: 55880414--55880438 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55880404 TTTAAAACAA
55880414 AATATTTTTAT
1 AATATTTTTAT
55880425 AATATTTTTAT
1 AATATTTTTAT
55880436 AAT
1 AAT
55880439 TCTTTTTGAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATATTTTTAT
Found at i:55881583 original size:15 final size:16
Alignment explanation
Indices: 55881565--55881594 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55881555 GGGAAAAGAA
55881565 AATAAA-TTAAAATAT
1 AATAAATTTAAAATAT
55881580 AATAAATTTAAAATA
1 AATAAATTTAAAATA
55881595 AAAAAGAATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAATTTAAAATAT
Found at i:55884159 original size:26 final size:28
Alignment explanation
Indices: 55884130--55884197 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
55884120 TTCAAAAGTC
*
55884130 TGTAGTACCTTTTTA-AATT-AAAAATA
1 TGTATTACCTTTTTATAATTAAAAAATA
**
55884156 TGTATTAAATTTTTATAATTAAAAAATA
1 TGTATTACCTTTTTATAATTAAAAAATA
*
55884184 TGCATTACCTTTTT
1 TGTATTACCTTTTT
55884198 TTTAATTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 12 0.35
27 4 0.12
28 18 0.53
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (28 bp):
TGTATTACCTTTTTATAATTAAAAAATA
Found at i:55892580 original size:10 final size:10
Alignment explanation
Indices: 55892565--55892596 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
55892555 TGTATAAACT
55892565 AATAGGACGA
1 AATAGGACGA
55892575 AATAGGACGA
1 AATAGGACGA
55892585 AATAGGACGA
1 AATAGGACGA
55892595 AA
1 AA
55892597 ATTAGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.28, T:0.09
Consensus pattern (10 bp):
AATAGGACGA
Found at i:55897056 original size:17 final size:18
Alignment explanation
Indices: 55897036--55897078 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
55897026 TAAAAAAATC
*
55897036 AAAATTTTAAAAA-ATAG
1 AAAATTATAAAAATATAG
*
55897053 AAAA-TATAAAAATATAT
1 AAAATTATAAAAATATAG
55897070 AAAATTATA
1 AAAATTATA
55897079 CAATATTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATTATAAAAATATAG
Found at i:55897355 original size:16 final size:15
Alignment explanation
Indices: 55897329--55897362 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
55897319 TATATATGAT
*
55897329 ATTTTCTTTAATTTA
1 ATTTTCTTTAATTAA
55897344 ATTTTACTTTAATTAA
1 ATTTT-CTTTAATTAA
55897360 ATT
1 ATT
55897363 ACATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTCTTTAATTAA
Found at i:55900665 original size:29 final size:29
Alignment explanation
Indices: 55900621--55900676 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
55900611 CAAACTTTTG
* * * *
55900621 GGGTGTTATTGTAATTTTTCTAAAGTTAA
1 GGGTGTTACTGCAATTTTACCAAAGTTAA
55900650 GGGTGTTACTGCAATTTTACCAAAGTT
1 GGGTGTTACTGCAATTTTACCAAAGTT
55900677 GGGGCACCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (29 bp):
GGGTGTTACTGCAATTTTACCAAAGTTAA
Found at i:55904236 original size:20 final size:20
Alignment explanation
Indices: 55904213--55904255 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
55904203 TGTAGATTTT
55904213 TTTTGGATTGTATTT-TATTA
1 TTTT-GATTGTATTTGTATTA
**
55904233 TTTTTCTTGTATTTGTATTA
1 TTTTGATTGTATTTGTATTA
55904253 TTT
1 TTT
55904256 GGGAGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.16, C:0.02, G:0.12, T:0.70
Consensus pattern (20 bp):
TTTTGATTGTATTTGTATTA
Found at i:55908525 original size:14 final size:14
Alignment explanation
Indices: 55908506--55908536 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55908496 GTCTGTTAAG
55908506 TATTAGTTAACAGT
1 TATTAGTTAACAGT
*
55908520 TATTAGTTAGCAGT
1 TATTAGTTAACAGT
55908534 TAT
1 TAT
55908537 AAATTAACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (14 bp):
TATTAGTTAACAGT
Found at i:55913485 original size:15 final size:15
Alignment explanation
Indices: 55913461--55913490 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55913451 ACACATTATA
*
55913461 TTCTATATATATAGT
1 TTCTAAATATATAGT
55913476 TTCTAAATATATAGT
1 TTCTAAATATATAGT
55913491 ATGCTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (15 bp):
TTCTAAATATATAGT
Found at i:55913888 original size:12 final size:10
Alignment explanation
Indices: 55913859--55913905 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
55913849 AATCAGAAGC
55913859 AAAATTTATT
1 AAAATTTATT
55913869 AAAATTTATT
1 AAAATTTATT
*
55913879 ATATAATTTATA
1 A-A-AATTTATT
55913891 AAAATTTTATT
1 AAAA-TTTATT
55913902 AAAA
1 AAAA
55913906 AATAACAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 13 0.41
11 11 0.34
12 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAAATTTATT
Found at i:55917443 original size:20 final size:21
Alignment explanation
Indices: 55917400--55917449 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
55917390 TGTCAATCCA
*
55917400 GTATCGATA-CTTTTCTTAAC
1 GTATCGATATATTTTCTTAAC
*
55917420 GTATCGATATATTTTC-TAAG
1 GTATCGATATATTTTCTTAAC
*
55917440 GTATCAATAT
1 GTATCGATAT
55917450 TCCTGCTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (21 bp):
GTATCGATATATTTTCTTAAC
Found at i:55918760 original size:50 final size:51
Alignment explanation
Indices: 55918635--55918881 Score: 189
Period size: 50 Copynumber: 4.8 Consensus size: 51
55918625 ATTTGGGTAA
* * *
55918635 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG--TATG
* * *
55918691 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG-ATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATG
* * * *
55918741 TGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACC-AATATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATG
** * * * * * * *
55918791 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGTA--GTA-CAGG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGTATG
* ** * *
55918840 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
55918882 TGTTATTATC
Statistics
Matches: 157, Mismatches: 31, Indels: 13
0.78 0.15 0.06
Matches are distributed among these distances:
49 37 0.24
50 77 0.49
53 3 0.02
55 1 0.01
56 39 0.25
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (51 bp):
AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATG
Found at i:55919098 original size:12 final size:12
Alignment explanation
Indices: 55919081--55919132 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
55919071 ATGAGTTATT
55919081 TAAGT-AAGCAAG
1 TAAGTAAAG-AAG
55919093 TAAGTAAAGAAG
1 TAAGTAAAGAAG
55919105 TAAG---AG-AG
1 TAAGTAAAGAAG
55919113 TAAGTAAAGAAG
1 TAAGTAAAGAAG
*
55919125 AAAGTAAA
1 TAAGTAAA
55919133 TATCATGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
11 2 0.06
12 21 0.62
13 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (12 bp):
TAAGTAAAGAAG
Found at i:55919107 original size:20 final size:20
Alignment explanation
Indices: 55919082--55919124 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
55919072 TGAGTTATTT
55919082 AAGTAAGCA-AGTAAGTAAAG
1 AAGTAAG-AGAGTAAGTAAAG
55919102 AAGTAAGAGAGTAAGTAAAG
1 AAGTAAGAGAGTAAGTAAAG
55919122 AAG
1 AAG
55919125 AAAGTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.56, C:0.02, G:0.28, T:0.14
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAG
Found at i:55922252 original size:31 final size:32
Alignment explanation
Indices: 55922217--55922279 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
55922207 ATCTTTATAC
* *
55922217 CTTAAATTGAAAAGGATTTTTA-TATAGGGGG
1 CTTAAATTGAAAAGGACTTTTATTAAAGGGGG
*
55922248 CTTAAATTGAAAATGACTTTTATTAAAGGGGG
1 CTTAAATTGAAAAGGACTTTTATTAAAGGGGG
55922280 AGCAACCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (32 bp):
CTTAAATTGAAAAGGACTTTTATTAAAGGGGG
Found at i:55924179 original size:25 final size:25
Alignment explanation
Indices: 55924099--55924180 Score: 62
Period size: 25 Copynumber: 3.3 Consensus size: 25
55924089 TAAACTCCTC
* *
55924099 CGAGCTGAATATC-AGTACGCTCATA
1 CGAGCTGAAAATCGA-TAAGCTCATA
** *
55924124 CGAGCTGAGTATCGGTAAGCTC-TCA
1 CGAGCTGAAAATCGATAAGCTCAT-A
*
55924149 CAAGCT-ACAAATCGATAAGCTCATA
1 CGAGCTGA-AAATCGATAAGCTCATA
55924174 CGAGCTG
1 CGAGCTG
55924181 CGGTTAGTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
24 2 0.05
25 41 0.93
26 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (25 bp):
CGAGCTGAAAATCGATAAGCTCATA
Found at i:55931860 original size:25 final size:24
Alignment explanation
Indices: 55931832--55931911 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
55931822 TGAACTCCTC
55931832 CGAGCTAAATATCGGTAAGCTCATA
1 CGAGCTAAA-ATCGGTAAGCTCATA
* * *
55931857 CGAGCTGAGATCAGTAAGCTC-TCA
1 CGAGCTAAAATCGGTAAGCTCAT-A
* *
55931881 TGAGCTACAAATTGGTAAGCTCATA
1 CGAGCTA-AAATCGGTAAGCTCATA
*
55931906 CAAGCT
1 CGAGCT
55931912 GCGATGAGTC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
23 1 0.02
24 17 0.40
25 23 0.55
26 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (24 bp):
CGAGCTAAAATCGGTAAGCTCATA
Found at i:55933851 original size:373 final size:373
Alignment explanation
Indices: 55933159--55933913 Score: 1420
Period size: 373 Copynumber: 2.0 Consensus size: 373
55933149 ACACTCCCTA
*
55933159 TCGATGATTTTGAGTTGACCCTTTCGAGCTAACAATTTTGCTTTTACATTTTGAGGGTTCTTGGT
1 TCGATGATTTTGAGTTGACCCTTTCGAGCTAACAATTTTGCGTTTACATTTTGAGGGTTCTTGGT
55933224 TTTTGGGTTTTGGGGTTTAATTTTTGTCTCCATCTTTTGTACTCTTCGTTCTTTTGCCATTATAG
66 TTTTGGGTTTTGGGGTTTAATTTTTGTCTCCATCTTTTGTACTCTTCGTTCTTTTGCCATTATAG
*
55933289 TAAAATTACATTTGCTTGTCGTTTTTTATGCTCTTTAGAGGGGGGTTTCCATGTTTAATTTGTGT
131 TAAAATTACATTTGCTCGTCGTTTTTTATGCTCTTTAGAGGGGGGTTTCCATGTTTAATTTGTGT
55933354 GTTCAATTTCTCATTTTATTCAGCTATTTTTACTTGTTCATTGTTTAATTTAGTCGATCTCCAAC
196 GTTCAATTTCTCATTTTATTCAGCTATTTTTACTTGTTCATTGTTTAATTTAGTCGATCTCCAAC
* *
55933419 AGGTGGTTTCAGAGCTAGTTCAATTTTCGTAGATCAGCCCATTCATATATGGTAGCAATAAGGTT
261 AAGTGGTTTCAGAGCTAGTTCAATTTTCGTAGATCAGCCCATTCATATATGGCAGCAATAAGGTT
55933484 TGACATTGAGAAGTTTGATGGTGTTACAAATTTCAATATGTGGCAAGT
326 TGACATTGAGAAGTTTGATGGTGTTACAAATTTCAATATGTGGCAAGT
55933532 TCGATGATTTTGAGTTGACCCTTTCGAGCTAACAATTTTGCGTTTACATTTTGAGGGTTCTTGGT
1 TCGATGATTTTGAGTTGACCCTTTCGAGCTAACAATTTTGCGTTTACATTTTGAGGGTTCTTGGT
*
55933597 TTTTGGGTTTTGGGGTTTAGTTTTTGTCTCCATCTTTTGTACTCTTCGTTCTTTTGCCATTATAG
66 TTTTGGGTTTTGGGGTTTAATTTTTGTCTCCATCTTTTGTACTCTTCGTTCTTTTGCCATTATAG
* * * *
55933662 TAAAATTACATTTGCTCGTGGTTTTTTATGCTCTTTAGAGGGGGTTTTCCGTGTTTAATTTTTGT
131 TAAAATTACATTTGCTCGTCGTTTTTTATGCTCTTTAGAGGGGGGTTTCCATGTTTAATTTGTGT
55933727 GTTCAATTTCTCATTTTATTCAGCTATTTTTACTTGTTCATTGTTTAATTTAGTCGATCTCCAAC
196 GTTCAATTTCTCATTTTATTCAGCTATTTTTACTTGTTCATTGTTTAATTTAGTCGATCTCCAAC
55933792 AAGTGGTTTCAGAGCTAGTTCAATTTTCGTAGATCAGCCCATTCATATATGGCAGCAATAAGGTT
261 AAGTGGTTTCAGAGCTAGTTCAATTTTCGTAGATCAGCCCATTCATATATGGCAGCAATAAGGTT
55933857 TGACATTGAGAAGTTTGATGGTGTTACAAATTTCAATATGTGGCAAGT
326 TGACATTGAGAAGTTTGATGGTGTTACAAATTTCAATATGTGGCAAGT
55933905 TCGAATGAT
1 TCG-ATGAT
55933914 GGCAATTTTA
Statistics
Matches: 372, Mismatches: 9, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
373 367 0.99
374 5 0.01
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (373 bp):
TCGATGATTTTGAGTTGACCCTTTCGAGCTAACAATTTTGCGTTTACATTTTGAGGGTTCTTGGT
TTTTGGGTTTTGGGGTTTAATTTTTGTCTCCATCTTTTGTACTCTTCGTTCTTTTGCCATTATAG
TAAAATTACATTTGCTCGTCGTTTTTTATGCTCTTTAGAGGGGGGTTTCCATGTTTAATTTGTGT
GTTCAATTTCTCATTTTATTCAGCTATTTTTACTTGTTCATTGTTTAATTTAGTCGATCTCCAAC
AAGTGGTTTCAGAGCTAGTTCAATTTTCGTAGATCAGCCCATTCATATATGGCAGCAATAAGGTT
TGACATTGAGAAGTTTGATGGTGTTACAAATTTCAATATGTGGCAAGT
Found at i:55937874 original size:20 final size:20
Alignment explanation
Indices: 55937849--55937888 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55937839 AATATTTTTC
*
55937849 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55937869 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55937889 TCATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55937890 original size:34 final size:35
Alignment explanation
Indices: 55937837--55937903 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
55937827 CAAACACCAG
* * *
55937837 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
55937872 AAAACATTTTCCAG-AAATCATTTTACAAAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAA
55937904 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
Found at i:55945072 original size:40 final size:40
Alignment explanation
Indices: 55945021--55945365 Score: 548
Period size: 40 Copynumber: 8.6 Consensus size: 40
55945011 CATTTGAATG
55945021 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
55945061 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
55945101 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
55945141 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
55945181 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* **
55945221 ATATCCGGGCTAAGACCCGACGGTGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
55945261 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * * *
55945301 ATATTCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
55945341 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
55945366 ATTGAGCTTG
Statistics
Matches: 282, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
39 2 0.01
40 279 0.99
41 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:55954540 original size:45 final size:45
Alignment explanation
Indices: 55954479--55954640 Score: 243
Period size: 45 Copynumber: 3.6 Consensus size: 45
55954469 TTGAAAAAAC
**
55954479 GAATAAGACCATAGTTGAAAGACACCGTGACACTATACCGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGACACTATACCGGAAAT
* * *
55954524 AAATAAGACCATAGTTGAAAGACATTATGGCACTATACCGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGACACTATACCGGAAAT
* * *
55954569 GAATAAAACCATAGTTGAAAGTCACTATGACACTATAACGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGACACTATACCGGAAAT
*
55954614 GAATAAGACCTTAGTTGAAAGACACTA
1 GAATAAGACCATAGTTGAAAGACACTA
55954641 AGGCAACATG
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 103 1.00
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.21
Consensus pattern (45 bp):
GAATAAGACCATAGTTGAAAGACACTATGACACTATACCGGAAAT
Found at i:55954659 original size:45 final size:44
Alignment explanation
Indices: 55954479--55954680 Score: 226
Period size: 45 Copynumber: 4.5 Consensus size: 44
55954469 TTGAAAAAAC
** *
55954479 GAATAAGACCATAGTTGAAAGACACCGTGACACTATACCGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCACTATA-CGGAAAT
* *
55954524 AAATAAGACCATAGTTGAAAGACATTATGGCACTATACCGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCACTATA-CGGAAAT
* * *
55954569 GAATAAAACCATAGTTGAAAGTCACTATGACACTATAACGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCACTAT-ACGGAAAT
* * *
55954614 GAATAAGACCTTAGTTGAAAGACACTAAGGCAAC-ATGACGAAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGC-ACTAT-ACGGAAAT
* * *
55954659 GAATAGGACCATAATGGAAAGA
1 GAATAAGACCATAGTTGAAAGA
55954681 TCCAGCGTCC
Statistics
Matches: 134, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 131 0.98
46 3 0.02
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (44 bp):
GAATAAGACCATAGTTGAAAGACACTATGGCACTATACGGAAAT
Found at i:55954670 original size:90 final size:90
Alignment explanation
Indices: 55954474--55954680 Score: 256
Period size: 90 Copynumber: 2.3 Consensus size: 90
55954464 TTCGCTTGAA
* * *
55954474 AAAACGAATAAGACCATAGTTGAAAGACACCGTGACACTATACCGGAAATAAATAAGACCATAGT
1 AAAATGAATAAGACCATAGTTGAAAGACACCATGACACTATAACGGAAATAAATAAGACCATAGT
* *
55954539 TGAAAGACATTATGGCACTATACCG
66 TGAAAGACACTAAGGCACTATACCG
* * * * * *
55954564 GAAATGAATAAAACCATAGTTGAAAGTCACTATGACACTATAACGGAAATGAATAAGACCTTAGT
1 AAAATGAATAAGACCATAGTTGAAAGACACCATGACACTATAACGGAAATAAATAAGACCATAGT
55954629 TGAAAGACACTAAGGCAAC-ATGA-CG
66 TGAAAGACACTAAGGC-ACTAT-ACCG
* * *
55954654 AAAATGAATAGGACCATAATGGAAAGA
1 AAAATGAATAAGACCATAGTTGAAAGA
55954681 TCCAGCGTCC
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
90 95 0.97
91 3 0.03
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (90 bp):
AAAATGAATAAGACCATAGTTGAAAGACACCATGACACTATAACGGAAATAAATAAGACCATAGT
TGAAAGACACTAAGGCACTATACCG
Found at i:55955534 original size:16 final size:17
Alignment explanation
Indices: 55955515--55955549 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
55955505 GATTAAAAAT
55955515 TTAAGGGTTTTGA-AGG
1 TTAAGGGTTTTGAGAGG
55955531 TTAAGGGTTTTGAGAGG
1 TTAAGGGTTTTGAGAGG
55955548 TT
1 TT
55955550 TTAGAGGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (17 bp):
TTAAGGGTTTTGAGAGG
Found at i:55959273 original size:19 final size:18
Alignment explanation
Indices: 55959249--55959301 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
55959239 TTTATTAAAG
55959249 AAAGGAAACAAAATAACTA
1 AAAGGAAACAAAATAA-TA
* *
55959268 AAAGGAATCTAAATCAATA
1 AAAGGAAACAAAAT-AATA
*
55959287 AAATGAAA-AAAATAA
1 AAAGGAAACAAAATAA
55959302 AAAGATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 2 0.07
18 4 0.14
19 20 0.71
20 2 0.07
ACGTcount: A:0.68, C:0.08, G:0.09, T:0.15
Consensus pattern (18 bp):
AAAGGAAACAAAATAATA
Found at i:55963698 original size:40 final size:40
Alignment explanation
Indices: 55963615--55963784 Score: 168
Period size: 41 Copynumber: 4.2 Consensus size: 40
55963605 CAAACACATC
* * *
55963615 CCTTTTCATTTGTTATCCTTTCCGGAT-A-TCAC-TTTCAA
1 CCTTTTCATGTGTTATCCTTTTCGAATAACTC-CTTTTCAA
* * * *
55963653 ACTTTTCATTTGATATCCTTTTTGAATATA-TCCTTTTCAA
1 CCTTTTCATGTGTTATCCTTTTCGAATA-ACTCCTTTTCAA
* *
55963693 CCTTTTCATGTGTTATCCTTTTCGGATAACTTTCTTTTCAA
1 CCTTTTCATGTGTTATCCTTTTCGAATAAC-TCCTTTTCAA
* *
55963734 CATTTTCATGTGTTATTCTTTTCGAATAACTTCCTTTTCAA
1 CCTTTTCATGTGTTATCCTTTTCGAATAAC-TCCTTTTCAA
*
55963775 CCATTTCATG
1 CCTTTTCATG
55963785 GATTCGAAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 22 0.20
39 2 0.02
40 32 0.29
41 54 0.49
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.50
Consensus pattern (40 bp):
CCTTTTCATGTGTTATCCTTTTCGAATAACTCCTTTTCAA
Found at i:55964810 original size:21 final size:21
Alignment explanation
Indices: 55964784--55964826 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55964774 GATATGGTAT
55964784 ATTTATTCATTAAATCCGTTA
1 ATTTATTCATTAAATCCGTTA
*
55964805 ATTTATTCATTAAATTCGTTA
1 ATTTATTCATTAAATCCGTTA
55964826 A
1 A
55964827 CTTAAGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTATTCATTAAATCCGTTA
Found at i:55967884 original size:15 final size:15
Alignment explanation
Indices: 55967864--55967900 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
55967854 GTGAAGTGTT
*
55967864 AAATGTTGATAAAAC
1 AAATGTCGATAAAAC
55967879 AAATGTCGATAAAAC
1 AAATGTCGATAAAAC
55967894 AAATGTC
1 AAATGTC
55967901 AAGTGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (15 bp):
AAATGTCGATAAAAC
Found at i:55968149 original size:23 final size:23
Alignment explanation
Indices: 55968076--55968158 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
55968066 ATTATTTCTA
55968076 TACG-TGCAAGTGATAATGGCAC
1 TACGATGCAAGTGATAATGGCAC
* * *
55968098 TACGTTGCAAGTGAAAATGACAC
1 TACGATGCAAGTGATAATGGCAC
* *
55968121 TACGATGCAAGTGTTAGTGGCAC
1 TACGATGCAAGTGATAATGGCAC
* *
55968144 TTCGATACAAAGTGA
1 TACGATGC-AAGTGA
55968159 CATCCTCATA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
22 4 0.08
23 40 0.82
24 5 0.10
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (23 bp):
TACGATGCAAGTGATAATGGCAC
Found at i:55969497 original size:29 final size:29
Alignment explanation
Indices: 55969468--55969541 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
55969458 TATTAATATA
*
55969468 AATAATATTA-GAATATTTTTATTTTTAT
1 AATAATATTATAAATATTTTTATTTTTAT
* *
55969496 AATTATTTTATAAATATTTTTATTTTT-T
1 AATAATATTATAAATATTTTTATTTTTAT
* *
55969524 GAATTATTTTATAAATAT
1 -AATAATATTATAAATAT
55969542 AATAAGGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.22
29 32 0.78
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
AATAATATTATAAATATTTTTATTTTTAT
Found at i:55969503 original size:12 final size:12
Alignment explanation
Indices: 55969486--55969518 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
55969476 TAGAATATTT
55969486 TTATTTTTATAA
1 TTATTTTTATAA
55969498 TTA-TTTTATAA
1 TTATTTTTATAA
*
55969509 ATATTTTTAT
1 TTATTTTTAT
55969519 TTTTTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTTTTATAA
Found at i:55969506 original size:11 final size:11
Alignment explanation
Indices: 55969490--55969537 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
55969480 ATATTTTTAT
55969490 TTTTATAATTA
1 TTTTATAATTA
*
55969501 TTTTATAAATA
1 TTTTATAATTA
55969512 TTTT-T-ATT-
1 TTTTATAATTA
*
55969520 TTTT-GAATTA
1 TTTTATAATTA
55969530 TTTTATAA
1 TTTTATAA
55969538 ATATAATAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
8 4 0.13
9 5 0.17
10 5 0.17
11 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTTATAATTA
Found at i:55987720 original size:44 final size:44
Alignment explanation
Indices: 55987672--55987760 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
55987662 TTAGAAAACT
*
55987672 ATGAAGTTTTACTGAAAAATATGCAAAA-TCTATAAACAAAACCC
1 ATGAAATTTTACTGAAAAATATGCAAAACT-TATAAACAAAACCC
* * *
55987716 ATGAAATTTTACTGAATAATGTTCAAAACTTATAAACAAAACCC
1 ATGAAATTTTACTGAAAAATATGCAAAACTTATAAACAAAACCC
55987760 A
1 A
55987761 GAATAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (44 bp):
ATGAAATTTTACTGAAAAATATGCAAAACTTATAAACAAAACCC
Found at i:55992766 original size:34 final size:34
Alignment explanation
Indices: 55992727--55992796 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
55992717 TATTCTGTTG
55992727 TGCGGAAGCGTGTAAAAGAGTAAAATTATTGTAC
1 TGCGGAAGCGTGTAAAAGAGTAAAATTATTGTAC
55992761 TGCGGAAGCGTGTAAAAGAGTAAAATTATTGTAC
1 TGCGGAAGCGTGTAAAAGAGTAAAATTATTGTAC
55992795 TG
1 TG
55992797 AAAAATTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (34 bp):
TGCGGAAGCGTGTAAAAGAGTAAAATTATTGTAC
Found at i:55998452 original size:42 final size:42
Alignment explanation
Indices: 55998405--55998488 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
55998395 TGGTAGTCTT
55998405 TGTATATCTATTAGGTGGATAGATAAAAAAAAATATTATTAA
1 TGTATATCTATTAGGTGGATAGATAAAAAAAAATATTATTAA
55998447 TGTATATCTATTAGGTGGATAGATAAAAAAAAATATTATTAA
1 TGTATATCTATTAGGTGGATAGATAAAAAAAAATATTATTAA
55998489 GTAATAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (42 bp):
TGTATATCTATTAGGTGGATAGATAAAAAAAAATATTATTAA
Found at i:56002570 original size:43 final size:43
Alignment explanation
Indices: 56002523--56002622 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
56002513 TTAGGGTCTT
*
56002523 TAGCGGCAC-TTTTCCTACAAATGCCGCTAAAGAACATGATCTG
1 TAGCGGCACTTTTTCC-ACAAACGCCGCTAAAGAACATGATCTG
* * * *
56002566 TAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGACCTT
1 TAGCGGCACTTTTTCCACAAACGCCGCTAAAGAACATGATCTG
* *
56002609 TAGTGGCGCTTTTT
1 TAGCGGCACTTTTT
56002623 TAAAAATGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 44 0.88
44 6 0.12
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
TAGCGGCACTTTTTCCACAAACGCCGCTAAAGAACATGATCTG
Found at i:56003001 original size:21 final size:21
Alignment explanation
Indices: 56002956--56003004 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
56002946 TCTACGCTGC
*
56002956 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCA
*
56002977 TCTGCTTCTCTCGCTGTC-GCA
1 TCTGCTTCCCTCGCTG-CAGCA
56002998 TCTGCTT
1 TCTGCTT
56003005 TAAGCTACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCA
Found at i:56003343 original size:29 final size:29
Alignment explanation
Indices: 56003311--56003414 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 29
56003301 CTATCACTGG
56003311 AAGTTATTTATGTAGGCTATGTATTATGC
1 AAGTTATTTATGTAGGCTATGTATTATGC
* * *
56003340 AAGTTATTTATGTAAG-TGGTGTATTATGT
1 AAGTTATTTATGTAGGCT-ATGTATTATGC
56003369 AAGTTATGTAAGTTATGTAGGCTATGTATTAT-C
1 AAGTTA--T---TTATGTAGGCTATGTATTATGC
56003402 TAAGTT-TTTATGT
1 -AAGTTATTTATGT
56003415 TATTATGTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
28 7 0.11
29 30 0.49
31 2 0.03
34 21 0.34
35 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (29 bp):
AAGTTATTTATGTAGGCTATGTATTATGC
Found at i:56003375 original size:9 final size:9
Alignment explanation
Indices: 56003363--56003436 Score: 55
Period size: 9 Copynumber: 8.2 Consensus size: 9
56003353 AAGTGGTGTA
56003363 TTATGTAAG
1 TTATGTAAG
56003372 TTATGTAAG
1 TTATGTAAG
*
56003381 TTATGTAGG
1 TTATGTAAG
*
56003390 CTATGT-A-
1 TTATGTAAG
*
56003397 TTATCTAAG
1 TTATGTAAG
*
56003406 TTTTTATGTTA-
1 ---TTATGTAAG
56003417 TTATGTAAG
1 TTATGTAAG
*
56003426 TTATGCAAG
1 TTATGTAAG
56003435 TT
1 TT
56003437 TCTATATAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
7 4 0.08
8 8 0.16
9 32 0.64
12 6 0.12
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:56003387 original size:25 final size:25
Alignment explanation
Indices: 56003347--56003436 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 25
56003337 TGCAAGTTAT
**
56003347 TTATGTAAGTGGTGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
*
56003372 TTATGTAAGTTATGTAGGCTATGT-A-
1 TTATGTAAGTTATGTA--TTATGTAAG
*
56003397 TTATCTAAGTTTTTATGTTATTATGTAAG
1 TTATGTAAG---TTATG-TATTATGTAAG
*
56003426 TTATGCAAGTT
1 TTATGTAAGTT
56003437 TCTATATAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
25 22 0.44
26 3 0.06
27 10 0.20
28 6 0.12
29 9 0.18
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTAAG
Found at i:56003430 original size:63 final size:63
Alignment explanation
Indices: 56003318--56003436 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
56003308 TGGAAGTTAT
* *
56003318 TTATGTAGGCTATGTATTATGCAAGTTATTTATGTAAGTGGTGTATTATGTAAGTTATGTAAG
1 TTATGTAGGCTATGTATTATGCAAGTTATTTATGTAAGTGATGTATTATGCAAGTTATGTAAG
* *
56003381 TTATGTAGGCTATGTATTAT-CTAAGTT-TTTATGTTA-TTATGTAAGTTATGCAAGTT
1 TTATGTAGGCTATGTATTATGC-AAGTTATTTATGTAAGTGATGT-A-TTATGCAAGTT
56003437 TCTATATAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
61 4 0.08
62 10 0.20
63 35 0.71
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (63 bp):
TTATGTAGGCTATGTATTATGCAAGTTATTTATGTAAGTGATGTATTATGCAAGTTATGTAAG
Found at i:56003534 original size:16 final size:17
Alignment explanation
Indices: 56003510--56003543 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
56003500 AATAAAAATT
*
56003510 TTATTTAAGT-TATGTA
1 TTATGTAAGTGTATGTA
56003526 TTATGTAAGTGTATGTA
1 TTATGTAAGTGTATGTA
56003543 T
1 T
56003544 AAGTTATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (17 bp):
TTATGTAAGTGTATGTA
Found at i:56003611 original size:19 final size:19
Alignment explanation
Indices: 56003589--56003630 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56003579 TGATATGATT
*
56003589 TATAAGTTTTGAAA-AAATA
1 TATAAATTTT-AAATAAATA
*
56003608 TATAAATTTTAAATATATA
1 TATAAATTTTAAATAAATA
56003627 TATA
1 TATA
56003631 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TATAAATTTTAAATAAATA
Found at i:56007751 original size:115 final size:114
Alignment explanation
Indices: 56007540--56008037 Score: 590
Period size: 114 Copynumber: 4.4 Consensus size: 114
56007530 TTAGGTTTTT
* * * * * * *
56007540 GCGGCGCTTTACTT-AAAACGCCGCTAAATAACCCGAAAACTAAGAAAACGGCGTCGTTGCGTTT
1 GCGGCGCTTTA-TTAAAAACGCCGCTAAAT-CCCCGAAAGCTCACAAAACGGCATCGTTGGGCTT
* * * **
56007604 A-GTTTTTTTAGTGGCGCTTT-TGAGCAAACGCCGCTAAAAGGTCTGAGCATTA
64 ATGTTTTTTT-GCGGCGCTTTCTCA-AAAACGCCGCT-AAAGCCCTGAGCATTA
* * *
56007656 GCGGCGCTTTATTAGAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCATTGGGCTTAG
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
* * * * *
56007721 GTTTTTTTGCGGCGCTTTATCAAAACCGCCGCCAAAACACTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
56007770 GCGGCGCTTTACTAAAAACGCCGCTAAATTCCCGAAAGCTCACAAAACGACATCGTTGGGCATAT
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
*
56007835 GTTTTTTTGCGGCGCTTTCTCAAAAACGCTGCTAAAGCCCTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * * *
56007884 GCGGCGCTTTATAAAAAACGCCGCTAAATCCCC-AAATGCTCAGAGAATGGCATCGTTGGGATTA
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAA-GCTCACAAAACGGCATCGTTGGGCTTA
* *
56007948 TGTTTTTTTGCGGCGCTTGCTTAAAAACGCCGCTAAAGCCCTGAGCATTA
65 TGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
56007998 GCGGCGATTTCTTACAAACGCCGCTAAATCCCCAAAAGCT
1 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCT
56008038 GAGGGAATGC
Statistics
Matches: 331, Mismatches: 46, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
113 3 0.01
114 244 0.74
115 49 0.15
116 35 0.11
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:56009853 original size:42 final size:44
Alignment explanation
Indices: 56009806--56009916 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 44
56009796 GTCTTAAACT
* *
56009806 GTGTAACTCACTGACTTAGTTCACACAACAG-TATGT-CAGGCC
1 GTGTAACTCACTGACTTAGTTCACACAACAGCCATGTCCAGACC
* *
56009848 GTGTAACTCTCTGACTT-GAT-ACAC-ACAGCCATGTCGCAGACC
1 GTGTAACTCACTGACTTAGTTCACACAACAGCCATGTC-CAGACC
* * *
56009890 GTGTAACTCACTAACTTAATACACACA
1 GTGTAACTCACTGACTTAGTTCACACA
56009917 GCCTTGTCGC
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
39 4 0.07
40 8 0.15
41 2 0.04
42 36 0.67
44 4 0.07
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (44 bp):
GTGTAACTCACTGACTTAGTTCACACAACAGCCATGTCCAGACC
Found at i:56009917 original size:42 final size:42
Alignment explanation
Indices: 56009846--56009933 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
56009836 GTATGTCAGG
* * * *
56009846 CCGTGTAACTCTCTGACTTGATACACACAGCCATGTCGCAGA
1 CCGTGTAACTCACTAACTTAATACACACAGCCATGTCGCAAA
*
56009888 CCGTGTAACTCACTAACTTAATACACACAGCCTTGTCGCAAA
1 CCGTGTAACTCACTAACTTAATACACACAGCCATGTCGCAAA
56009930 CCGT
1 CCGT
56009934 ATACGGGCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (42 bp):
CCGTGTAACTCACTAACTTAATACACACAGCCATGTCGCAAA
Found at i:56012716 original size:21 final size:22
Alignment explanation
Indices: 56012692--56012733 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
56012682 ATGAGGTCTT
*
56012692 AAAATCGATGGA-AACAAGAAG
1 AAAATCGATGGAGAAAAAGAAG
*
56012713 AAAATTGATGGAGAAAAAGAA
1 AAAATCGATGGAGAAAAAGAA
56012734 TTTAGTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.05, G:0.24, T:0.12
Consensus pattern (22 bp):
AAAATCGATGGAGAAAAAGAAG
Found at i:56014178 original size:10 final size:10
Alignment explanation
Indices: 56014146--56014170 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56014136 CTCAATAAAC
56014146 AAAAAAAGAA
1 AAAAAAAGAA
56014156 AAAAAAAGAA
1 AAAAAAAGAA
56014166 AAAAA
1 AAAAA
56014171 GGGAAAAAGA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:56014419 original size:3 final size:3
Alignment explanation
Indices: 56014411--56014440 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
56014401 TCTCTGATTC
56014411 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
56014441 CTCTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:56054702 original size:28 final size:27
Alignment explanation
Indices: 56054640--56054789 Score: 214
Period size: 28 Copynumber: 5.6 Consensus size: 27
56054630 TTATTAAGTC
* *
56054640 CGCACACTCAGTGCTATATAAT-AACT
1 CGCACACTTAGTGCTACATAATCAACT
56054666 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
56054694 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
56054721 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
56054749 CGCACACTTAGTGCTACAT-ATTAATT
1 CGCACACTTAGTGCTACATAATCAACT
56054775 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
56054790 GCACAATTTA
Statistics
Matches: 115, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
26 38 0.33
27 28 0.24
28 49 0.43
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:56054731 original size:55 final size:53
Alignment explanation
Indices: 56054640--56054814 Score: 224
Period size: 55 Copynumber: 3.2 Consensus size: 53
56054630 TTATTAAGTC
* * *
56054640 CGCACACTCAGTGCTATATAATAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACAT-ATAACTCGCACACTTAGTGCTACATAATCAAACT
*
56054694 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATA-T-AACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
56054749 CGCACACTTAGTGCTACATATTAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATA-TAACTCGCACACTTAGTGCTACATAA-TCAAACT
56054804 CGCACACTTAG
1 CGCACACTTAG
56054815 CGCCAATCTC
Statistics
Matches: 107, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.36
55 67 0.63
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATATAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:56054809 original size:83 final size:81
Alignment explanation
Indices: 56054639--56054814 Score: 214
Period size: 83 Copynumber: 2.1 Consensus size: 81
56054629 TTTATTAAGT
* *
56054639 CCGCACACTCAGTGCTATATAATAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
1 CCGCACACTTAGTGCTACATAATAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
*
56054704 GTGCTACATAGTCAAC
66 GTGCTACATAGTAAAC
* * * *
56054720 TCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACAT-ATTA-ATTCGCACACT
1 CCGCACACTTAGTGCTACATAAT--AACTCGCACACTTAGTGCTACATAATCATACTCGCACACT
*
56054783 TAGTGCTGCACA-ATTTAAAC
64 TAGTGCT--ACATA-GTAAAC
56054803 CCGCACACTTAG
1 CCGCACACTTAG
56054815 CGCCAATCTC
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
81 36 0.44
82 4 0.05
83 41 0.51
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (81 bp):
CCGCACACTTAGTGCTACATAATAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
GTGCTACATAGTAAAC
Found at i:56062705 original size:28 final size:27
Alignment explanation
Indices: 56062641--56062792 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
56062631 TTATTAAGTC
* *
56062641 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
56062668 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
56062696 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
56062723 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* * *
56062751 CGCACACTTAGTGCTACATATTTAATT
1 CGCACACTTAGTGCTACATAATCAACT
56062778 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
56062793 GCACAATTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 65 0.56
28 51 0.44
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:56062725 original size:55 final size:55
Alignment explanation
Indices: 56062641--56062817 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
56062631 TTATTAAGTC
* * *
56062641 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
*
56062696 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * * *
56062751 CGCACACTTAGTGCTACATATTTAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
56062807 CGCACACTTAG
1 CGCACACTTAG
56062818 CGCCAATCTC
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 94 0.85
56 16 0.15
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:56072794 original size:50 final size:52
Alignment explanation
Indices: 56072665--56072906 Score: 198
Period size: 50 Copynumber: 4.7 Consensus size: 52
56072655 AGGGATGAAA
**
56072665 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTATTAAGGATATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC---CGAGGATA-GAGAGG
*
56072721 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATA-AGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATAGAGAGG
* * * * **
56072771 TCCC-TCGTAAGACCATGTGTGGGACATGGCATGGGCACCGA-TAT-GAAAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATAGAGAGG
* * * * * * *
56072821 TCTCATGTAAGACCATATCTGGGATATGACATTTGCAGTAC-AGGA-A-ACA--
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGAGGATAGAGAGG
*
56072870 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
56072907 TGTTATTATC
Statistics
Matches: 153, Mismatches: 26, Indels: 21
0.76 0.13 0.10
Matches are distributed among these distances:
49 32 0.21
50 73 0.48
51 4 0.03
52 6 0.04
53 1 0.01
56 37 0.24
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (52 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATAGAGAGG
Found at i:56088042 original size:20 final size:20
Alignment explanation
Indices: 56088017--56088246 Score: 336
Period size: 20 Copynumber: 11.5 Consensus size: 20
56088007 AAGCTTATAC
*
56088017 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
56088037 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
56088057 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
56088077 CAAGTAAAAGAAACT-GAAAG
1 TAAGTAAATGAAA-TGGAAAG
*
56088097 TAAGTAAATGAAATAGAAAG
1 TAAGTAAATGAAATGGAAAG
*
56088117 TAAGTAAAAGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
56088137 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
** *
56088157 TAAACAAAAGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
*
56088177 TAAGTAAATGTAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
56088197 TAAGTAAATGTAATGGGAAG
1 TAAGTAAATGAAATGGAAAG
*
56088217 TAAGTAAATGTAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
56088237 TAAGTAAATG
1 TAAGTAAATG
56088247 GAGTGGTTCA
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
19 1 0.01
20 189 0.99
21 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.24, T:0.20
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:56088189 original size:10 final size:10
Alignment explanation
Indices: 56088176--56088246 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
56088166 GAAATGGAAA
56088176 GTAAGTAAAT
1 GTAAGTAAAT
*
56088186 GTAATGGAAA-
1 GTAA-GTAAAT
56088196 GTAAGTAAAT
1 GTAAGTAAAT
**
56088206 GTAATGGGAA-
1 GTAA-GTAAAT
56088216 GTAAGTAAAT
1 GTAAGTAAAT
*
56088226 GTAATGGAAA-
1 GTAA-GTAAAT
56088236 GTAAGTAAAT
1 GTAAGTAAAT
56088246 G
1 G
56088247 GAGTGGTTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 11 0.23
10 25 0.53
11 11 0.23
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (10 bp):
GTAAGTAAAT
Found at i:56093354 original size:48 final size:48
Alignment explanation
Indices: 56093283--56093375 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
56093273 TTTCTTTACT
*
56093283 TAAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAATAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAATAG
* *
56093331 TAAAAACGCCTAAGTCCGCCTAACTTGCAAAGATAAAGGATTCAA
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAA
56093376 CTGAATTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAATAG
Found at i:56093641 original size:17 final size:17
Alignment explanation
Indices: 56093585--56093645 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
56093575 CAAAAGCTAA
*
56093585 AATTAAAAGCTGTATAC
1 AATTAGAAGCTGTATAC
* *
56093602 AATTAGAA-CTCTAAGACAC
1 AATTAGAAGCTGT---ATAC
56093621 AATTAGAAGCTGTATAC
1 AATTAGAAGCTGTATAC
56093638 AATTAGAA
1 AATTAGAA
56093646 CTCTAAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (17 bp):
AATTAGAAGCTGTATAC
Found at i:56097299 original size:40 final size:40
Alignment explanation
Indices: 56097210--56097379 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
56097200 TCCTCGTTCA
* * * * *
56097210 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
56097249 CATGCCTTCGGGTCGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
56097289 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
56097329 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
56097369 AAGGCCTTCGG
1 AATGCCTTCGG
56097380 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 31 0.28
40 79 0.72
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:56101541 original size:48 final size:48
Alignment explanation
Indices: 56101460--56101553 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
56101450 TCTTTACTTA
* * *
56101460 AAAATGCCTAATTCAGCCTAACTCGCAATGATAAAGGATTCAACAGTG
1 AAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAGTG
* *
56101508 AAAACGCCTAAGTCGGCCTAACTTGCAAAGATAAAGGATTCAACAG
1 AAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAG
56101554 AATTCCCTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (48 bp):
AAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAGTG
Found at i:56101799 original size:19 final size:19
Alignment explanation
Indices: 56101775--56101828 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
56101765 AAAGCTGTAT
56101775 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
56101794 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
56101811 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
56101829 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:56101807 original size:36 final size:36
Alignment explanation
Indices: 56101760--56101828 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
56101750 CAAAGGCTAA
56101760 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAC
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAC
*
56101796 AATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGA
56101829 TTACATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (36 bp):
AATTAAAAGCTGTATACAATTAGAACTCTAAGACAC
Found at i:56101816 original size:17 final size:17
Alignment explanation
Indices: 56101760--56101820 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
56101750 CAAAGGCTAA
*
56101760 AATTAAAAGCTGTATAC
1 AATTAGAAGCTGTATAC
* *
56101777 AATTAGAA-CTCTAAGACAC
1 AATTAGAAGCTGT---ATAC
56101796 AATTAGAAGCTGTATAC
1 AATTAGAAGCTGTATAC
56101813 AATTAGAA
1 AATTAGAA
56101821 CTCTAAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (17 bp):
AATTAGAAGCTGTATAC
Found at i:56106317 original size:5 final size:5
Alignment explanation
Indices: 56106307--56106340 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
56106297 TATTTGTTAT
56106307 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
1 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
56106341 TATATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATA
Found at i:56107719 original size:18 final size:18
Alignment explanation
Indices: 56107688--56107735 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
56107678 TGTCGTTCGT
**
56107688 TTTCAAAACATTATTC-A
1 TTTCAAAATGTTATTCAA
*
56107705 TTTACAAATTGTTATTCAA
1 TTT-CAAAATGTTATTCAA
56107724 TTTCAAAATGTT
1 TTTCAAAATGTT
56107736 TTTTTATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (18 bp):
TTTCAAAATGTTATTCAA
Found at i:56109958 original size:18 final size:18
Alignment explanation
Indices: 56109937--56109978 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
56109927 AATTCGTTTT
56109937 CAAAACATTATTC-ATTCA
1 CAAAACATTATTCAATT-A
* *
56109955 CAAATCGTTATTCAATTA
1 CAAAACATTATTCAATTA
56109973 CAAAAC
1 CAAAAC
56109979 GGTTTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (18 bp):
CAAAACATTATTCAATTA
Found at i:56122466 original size:21 final size:21
Alignment explanation
Indices: 56122442--56122486 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56122432 CTACTGGTAT
*
56122442 AACTGTGAGTTCTACCAAGAC
1 AACTCTGAGTTCTACCAAGAC
* *
56122463 AACTCTGGGTTCTACCAATAC
1 AACTCTGAGTTCTACCAAGAC
56122484 AAC
1 AAC
56122487 CCAAACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
AACTCTGAGTTCTACCAAGAC
Found at i:56125620 original size:50 final size:50
Alignment explanation
Indices: 56125555--56125687 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
56125545 TAATGACATA
* ** * * *
56125555 TCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGACAACGCCATG
* *
56125605 TCCCAGATATGGTCTTA-AGGGGGACCTCTCATCTCGGTGACAACGCCATG
1 TCCCAGATATGGTCTTACA-TGGGACCTCTCATATCGGTGACAACGCCATG
* *
56125655 TCCCAGACATGGTCTTACGTGGGACCTCTCATA
1 TCCCAGATATGGTCTTACATGGGACCTCTCATA
56125688 ACCTCAATAA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGACAACGCCATG
Found at i:56127105 original size:21 final size:21
Alignment explanation
Indices: 56127079--56127118 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56127069 TACTTTCACA
56127079 AGTGCAATACTTTTATTCCTT
1 AGTGCAATACTTTTATTCCTT
*
56127100 AGTGCAATACTTTTGTTCC
1 AGTGCAATACTTTTATTCC
56127119 ATAATACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (21 bp):
AGTGCAATACTTTTATTCCTT
Found at i:56132397 original size:13 final size:13
Alignment explanation
Indices: 56132375--56132413 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
56132365 AAGTTCTTAG
56132375 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
*
56132388 TTCTTCTTTTCTT
1 TTCTTTTTTTCTT
*
56132401 TTATTTTTTTCTT
1 TTCTTTTTTTCTT
56132414 ATTGTTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:56134610 original size:45 final size:45
Alignment explanation
Indices: 56134542--56134802 Score: 283
Period size: 45 Copynumber: 5.8 Consensus size: 45
56134532 TTGGTTTGAA
56134542 AAACGAATAAGACCATAAG-TGAAAGACACTATGGCACTATACCAG
1 AAACGAATAAGACCAT-AGTTGAAAGACACTATGGCACTATACCAG
*
56134587 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATA-CTG
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* * * ** *
56134631 AAAATGAATAAGACCATAATTGAAAGACACTATGTCACGCTACCAA
1 -AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* * *
56134677 AAATGAATAAGACCATAGTTGAAAGACACTACGGCACTGTACCAG
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* * * * ***
56134722 AAACGAATAAGACCATACTTGAATGACACAATGGCATTATGTTAG
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* ** * * *
56134767 AGATAAATAAGACTATGGCTGAAAGACACTATGGCA
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCA
56134803 TCTCTGAACA
Statistics
Matches: 180, Mismatches: 33, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
44 4 0.02
45 175 0.97
46 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (45 bp):
AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
Found at i:56134790 original size:135 final size:135
Alignment explanation
Indices: 56134540--56134799 Score: 353
Period size: 135 Copynumber: 1.9 Consensus size: 135
56134530 TATTGGTTTG
* *
56134540 AAAAACGAATAAGACCATAAGTGAAAGACACTATGGCACTATACCAGAAACGAATAAGACCATAG
1 AAAAACGAATAAGACCATAAGTGAAAGACACTACGGCACTATACCAGAAACGAATAAGACCATAC
* * *
56134605 TTGAAAGACACTATGGCACTATACTGAAAATGAATAAGACCATAATTGAAAGACACTATGTCACG
66 TTGAAAGACACAATGGCACTATACTGAAAATAAATAAGACCATAACTGAAAGACACTATGTCACG
56134670 CTACC
131 CTACC
* *
56134675 AAAAATGAATAAGACCAT-AGTTGAAAGACACTACGGCACTGTACCAGAAACGAATAAGACCATA
1 AAAAACGAATAAGACCATAAG-TGAAAGACACTACGGCACTATACCAGAAACGAATAAGACCATA
* * * * * * **
56134739 CTTGAATGACACAATGGCATTAT-GTTAGAGATAAATAAGACTATGGCTGAAAGACACTATG
65 CTTGAAAGACACAATGGCACTATACTGA-AAATAAATAAGACCATAACTGAAAGACACTATG
56134800 GCATCTCTGA
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 4 0.04
135 104 0.96
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.20
Consensus pattern (135 bp):
AAAAACGAATAAGACCATAAGTGAAAGACACTACGGCACTATACCAGAAACGAATAAGACCATAC
TTGAAAGACACAATGGCACTATACTGAAAATAAATAAGACCATAACTGAAAGACACTATGTCACG
CTACC
Found at i:56134981 original size:40 final size:40
Alignment explanation
Indices: 56134903--56134994 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
56134893 TGTAAAATGA
*** *
56134903 ATATATGAAATGATTTTATGAATTGGTTCTATGAAAATAG
1 ATATATGAAATGATTTTATGAATCAATTATATGAAAATAG
*
56134943 ATATATTG-AATGATTTTATGAATCAATTATATGTAAATA-
1 ATATA-TGAAATGATTTTATGAATCAATTATATGAAAATAG
*
56134982 ATAATATAAAATG
1 AT-ATATGAAATG
56134995 TTTATACGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
39 3 0.07
40 38 0.88
41 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (40 bp):
ATATATGAAATGATTTTATGAATCAATTATATGAAAATAG
Found at i:56138111 original size:15 final size:15
Alignment explanation
Indices: 56138091--56138120 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56138081 GCTAAGTGAT
56138091 AACATGGTGATTGAA
1 AACATGGTGATTGAA
56138106 AACATGGTGATTGAA
1 AACATGGTGATTGAA
56138121 GCATGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
AACATGGTGATTGAA
Found at i:56140501 original size:5 final size:5
Alignment explanation
Indices: 56140491--56140524 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
56140481 TATTTGTTAT
56140491 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
1 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
56140525 TATATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATA
Found at i:56151245 original size:24 final size:24
Alignment explanation
Indices: 56151218--56151268 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
56151208 GTAGGAGGTT
56151218 AATTTCATCTAAAATC-GATTAAAC
1 AATTTCATCTAAAATCAG-TTAAAC
56151242 AATTTCATCTAAAATCAGTTAAAC
1 AATTTCATCTAAAATCAGTTAAAC
56151266 AAT
1 AAT
56151269 AACCCAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
AATTTCATCTAAAATCAGTTAAAC
Found at i:56156965 original size:19 final size:19
Alignment explanation
Indices: 56156937--56156978 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56156927 TCATCAATTA
56156937 ATTTAATAAT-ATTACTATT
1 ATTTAATAATCA-TACTATT
* *
56156956 ATTTATTAATCATATTATT
1 ATTTAATAATCATACTATT
56156975 ATTT
1 ATTT
56156979 GTATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAATAATCATACTATT
Found at i:56159506 original size:45 final size:45
Alignment explanation
Indices: 56159414--56159507 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
56159404 AACCCCTGTT
* *
56159414 GTGCGAGCCCCTATCATGCGAACCCTAGTATAGGCCAGCCCTATC
1 GTGCGAGCCCCTATCATGCAAACCCTAGTATAAGCCAGCCCTATC
* * * *
56159459 GTGCGAGCCCCTATCTTGCAAACCCTAGTATAAGCGAGCCTTGTC
1 GTGCGAGCCCCTATCATGCAAACCCTAGTATAAGCCAGCCCTATC
56159504 GTGC
1 GTGC
56159508 AAACCCTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.22
Consensus pattern (45 bp):
GTGCGAGCCCCTATCATGCAAACCCTAGTATAAGCCAGCCCTATC
Found at i:56160300 original size:43 final size:43
Alignment explanation
Indices: 56160243--56160472 Score: 298
Period size: 43 Copynumber: 5.3 Consensus size: 43
56160233 ATTTTTAGAA
* **
56160243 ACAAACGCCACTAAAGACCGCGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * **
56160286 ACAAACGCCGCTAAAGACCAAGACCTTTAGCCGTGCTTTTATC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
*
56160329 ACAAAGGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * *
56160372 ACAAACGCTGCTAAAGCCCATGACCTTTAGCAGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * * *
56160415 ACAAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTCTCGC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
*
56160458 AAAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
56160473 AACATAGCCT
Statistics
Matches: 161, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 161 1.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.20
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
Found at i:56165194 original size:7 final size:7
Alignment explanation
Indices: 56165184--56165242 Score: 82
Period size: 7 Copynumber: 8.4 Consensus size: 7
56165174 CACTAACTCT
*
56165184 TAACCTC
1 TAACCCC
56165191 TAACCCC
1 TAACCCC
*
56165198 TAACCCT
1 TAACCCC
56165205 TAACCCC
1 TAACCCC
56165212 TAACCCC
1 TAACCCC
56165219 TAACCCC
1 TAACCCC
**
56165226 TAACTAC
1 TAACCCC
56165233 TAACCCC
1 TAACCCC
56165240 TAA
1 TAA
56165243 ACCTTATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.20
Consensus pattern (7 bp):
TAACCCC
Found at i:56165200 original size:21 final size:21
Alignment explanation
Indices: 56165176--56165248 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
56165166 CCATGAATCA
*
56165176 CTAACTCTTAACCTCTAACCC
1 CTAACCCTTAACCTCTAACCC
*
56165197 CTAACCCTTAACCCCTAACCC
1 CTAACCCTTAACCTCTAACCC
*
56165218 CTAACCCCTAA-CTACTAACCC
1 CTAACCCTTAACCT-CTAACCC
*
56165239 CTAAACCTTA
1 CTAACCCTTA
56165249 TTTAATATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAACCCTTAACCTCTAACCC
Found at i:56165355 original size:68 final size:70
Alignment explanation
Indices: 56165232--56165366 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 70
56165222 CCCCTAACTA
56165232 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
1 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
56165297 AATCC
66 AATCC
*
56165302 CTAACCCCTAAACCTTATTT-A-ATATAAATTAAAATACACTAATTAATCTAAACCTTAAACCCT
1 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
56165365 AA
66 AA
56165367 CCTAACATCG
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 43 0.67
69 1 0.02
70 20 0.31
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (70 bp):
CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
AATCC
Found at i:56165423 original size:7 final size:7
Alignment explanation
Indices: 56165411--56165442 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
56165401 CTCTTAATCT
56165411 CTAACCC
1 CTAACCC
*
56165418 CTAACCA
1 CTAACCC
56165425 CTAACCC
1 CTAACCC
56165432 CTAACCC
1 CTAACCC
56165439 CTAA
1 CTAA
56165443 ATCACAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:56165481 original size:14 final size:15
Alignment explanation
Indices: 56165462--56165494 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
56165452 CTTAAACCAG
56165462 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
56165476 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
56165491 AATC
1 AATC
56165495 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:56165881 original size:41 final size:41
Alignment explanation
Indices: 56165824--56165981 Score: 219
Period size: 41 Copynumber: 3.9 Consensus size: 41
56165814 AAATATTTTT
*
56165824 GCGGCGCTTTTTCAAAAACGCCGCTAAA-AGCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGA-CCCGAGCATCA
* * *
56165865 GCGGCGCTTTTTCAAAAACGCCGTTAAAGATCTGAGCATCA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATCA
* * *
56165906 GCGGTGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATCA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATCA
* *
56165947 GCGGCGCTTTTTCAAAAACGTCGCTAAAGCCCCGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGA
56165982 AAGGTCAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 104 0.99
42 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATCA
Found at i:56170419 original size:3 final size:3
Alignment explanation
Indices: 56170411--56170435 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56170401 ATTTGCATCC
56170411 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
56170436 AAACGGGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:56171363 original size:3 final size:3
Alignment explanation
Indices: 56171355--56171387 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
56171345 AAAGCACTTA
56171355 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56171388 GGGCATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56171479 original size:8 final size:8
Alignment explanation
Indices: 56171468--56171541 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
56171458 TATAAAAATA
56171468 TATATATG
1 TATATATG
56171476 TATATATG
1 TATATATG
56171484 TACGTATAT-
1 TA--TATATG
*
56171493 TA-AAAT-
1 TATATATG
*
56171499 TATA-AAG
1 TATATATG
*
56171506 TATA-ATA
1 TATATATG
56171513 TATATATG
1 TATATATG
* *
56171521 TAGATATA
1 TATATATG
56171529 TATATATG
1 TATATATG
56171537 TATAT
1 TATAT
56171542 GTAAGTTGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
6 6 0.12
7 10 0.19
8 29 0.56
9 2 0.04
10 5 0.10
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (8 bp):
TATATATG
Found at i:56171834 original size:23 final size:23
Alignment explanation
Indices: 56171789--56171840 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
56171779 CGTACATGTA
56171789 TATATGTATATATATTATAAAAG
1 TATATGTATATATATTATAAAAG
*
56171812 TGTATGTATATATAATTAT-AAAG
1 TATATGTATATAT-ATTATAAAAG
56171835 TATATG
1 TATATG
56171841 AAGTATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (23 bp):
TATATGTATATATATTATAAAAG
Found at i:56172464 original size:40 final size:40
Alignment explanation
Indices: 56172409--56172490 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
56172399 ATTAAAGATT
*
56172409 GACCAACCAAGAAGCAACAAGTTATACATGAACAATCAAC
1 GACCAACCAAGAAGCAACAAGTTATACATGAACAACCAAC
*
56172449 GACCAATCAAGAAGCAACAAGTTATACATGAACAACCAAC
1 GACCAACCAAGAAGCAACAAGTTATACATGAACAACCAAC
56172489 GA
1 GA
56172491 GCATGTGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.50, C:0.24, G:0.13, T:0.12
Consensus pattern (40 bp):
GACCAACCAAGAAGCAACAAGTTATACATGAACAACCAAC
Found at i:56175279 original size:40 final size:40
Alignment explanation
Indices: 56175168--56175321 Score: 132
Period size: 40 Copynumber: 3.9 Consensus size: 40
56175158 AGCAGCACTT
** * *
56175168 TTAGCGGCGTTTGGACAAAAAACGCCGGTAAAAATCAAGCA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAAT-AAGCA
** *** * * * *
56175209 TTAGCGGC-ACTTTATGGAAATCGCCACTAAAGATTGAGCA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAA-AATAAGCA
* *
56175249 TTAGTGGCGTTTTT-CAAAAAACGCCGCTAAAAATAAGCA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAATAAGCA
*
56175288 TTAGCGGCGTTTTTAAAAAAAACGCCGCAAAAAA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAA
56175322 CATAAGCCCA
Statistics
Matches: 85, Mismatches: 25, Indels: 7
0.73 0.21 0.06
Matches are distributed among these distances:
39 19 0.22
40 53 0.62
41 13 0.15
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAATAAGCA
Found at i:56175421 original size:41 final size:42
Alignment explanation
Indices: 56175357--56175675 Score: 354
Period size: 41 Copynumber: 7.8 Consensus size: 42
56175347 GACCTTTCGT
* * *
56175357 GGCTTTAACGGCGTTTTTAGAAAAGCGCTGCTAATGCCT-GG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
*
56175398 GTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCT--G
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
** * *
56175438 GTTTTTAGCGGCGTTTTTGGAAAAAGTGCCG-TAATG-GTAGG
1 GGCTTTAGCGGCGTTTTTGG-AAAAGCGCCGCTAATGCCTAGG
* **
56175479 GGCTTTAGTGGC-TTTTTGGAAAAGCGCCGCTAAT-TATAGG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
56175519 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTA--
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
** * * *
56175559 GATTTTAGCGGCGTTTTTGGAAAAAGTGTCGCTAATG-GTAGG
1 GGCTTTAGCGGCGTTTTTGG-AAAAGCGCCGCTAATGCCTAGG
* ** *
56175601 GGCTTTAGTGGCGTTTTTGGAAAAGCGCCGCTAAT-TATAAG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
*
56175642 GGCTTTAGCGCCGTTTTTGGAAAAGCGCCGCTAA
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
56175676 AAATATTTTA
Statistics
Matches: 238, Mismatches: 29, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
39 10 0.04
40 71 0.30
41 138 0.58
42 19 0.08
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (42 bp):
GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
Found at i:56176090 original size:21 final size:20
Alignment explanation
Indices: 56176056--56176096 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
56176046 TTATGTATCA
*
56176056 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
56176076 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
56176097 AGGGGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:56176098 original size:7 final size:7
Alignment explanation
Indices: 56176088--56176120 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
56176078 GATTTAAGGT
56176088 TTAGGGG
1 TTAGGGG
56176095 TTAGGGG
1 TTAGGGG
56176102 TTAGGGG
1 TTAGGGG
56176109 CTTAGGGG
1 -TTAGGGG
56176117 TTAG
1 TTAG
56176121 ACATTATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.15, C:0.03, G:0.52, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Done.