Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015494.1 Corchorus capsularis cultivar CVL-1 contig15515, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 119779
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:633 original size:109 final size:109
Alignment explanation
Indices: 437--711 Score: 419
Period size: 109 Copynumber: 2.5 Consensus size: 109
427 ACTATTATAG
* * *
437 TTTTATTCTACTAGAAACTATATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
502 TCTTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
551 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
616 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
*
660 CTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
712 TAATTTTTTT
Statistics
Matches: 153, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
108 7 0.05
109 121 0.79
110 3 0.02
111 2 0.01
114 20 0.13
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
Found at i:1845 original size:15 final size:15
Alignment explanation
Indices: 1825--1913 Score: 88
Period size: 16 Copynumber: 5.7 Consensus size: 15
1815 CGGGTTCGGG
*
1825 CGGGTTCGGGTACTT
1 CGGGTTCGGGTATTT
*
1840 CGGGTTCAGGTATTTT
1 CGGGTTCGGGTA-TTT
* *
1856 CGAGATCGGGTATTTT
1 CGGGTTCGGGTA-TTT
* *
1872 CGGGTTTGGGATTTTT
1 CGGGTTCGGG-TATTT
1888 CGGGTTCGGGTATTT
1 CGGGTTCGGGTATTT
*
1903 CGGATTCGGGT
1 CGGGTTCGGGT
1914 TCACTTTCGA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
15 25 0.42
16 34 0.57
17 1 0.02
ACGTcount: A:0.10, C:0.13, G:0.37, T:0.39
Consensus pattern (15 bp):
CGGGTTCGGGTATTT
Found at i:2695 original size:16 final size:16
Alignment explanation
Indices: 2676--2718 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
2666 TTGGGTCGGG
*
2676 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
2692 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATT
*
2708 TCAGGTTCGGG
1 TCGGGTTCGGG
2719 CGGGTTCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.09, C:0.14, G:0.40, T:0.37
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:8266 original size:30 final size:31
Alignment explanation
Indices: 8189--8266 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
8179 GAAATTGACA
* * *
8189 ATTGATCCCACTAAATTTGAAGTTTTATCAT
1 ATTGACCCCACTAAAATTGAAGTTTTATCAC
8220 ATTGACCCCACTAAAATTGAAGTTTTATCAC
1 ATTGACCCCACTAAAATTGAAGTTTTATCAC
*
8251 ATTGA-CCCTCTAAAAT
1 ATTGACCCCACTAAAAT
8267 AAAAGATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 10 0.23
31 33 0.77
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.36
Consensus pattern (31 bp):
ATTGACCCCACTAAAATTGAAGTTTTATCAC
Found at i:8277 original size:30 final size:30
Alignment explanation
Indices: 8189--8286 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
8179 GAAATTGACA
* ** * *
8189 ATTGATCCCACTAAATTTGAAGTTTTATCAT
1 ATTGA-CCCACTAAAATAAAAGATTTATCAC
** *
8220 ATTGACCCCACTAAAATTGAAGTTTTATCAC
1 ATTGA-CCCACTAAAATAAAAGATTTATCAC
*
8251 ATTGACCCTCTAAAATAAAAGATTTAT-AGC
1 ATTGACCCACTAAAATAAAAGATTTATCA-C
8281 ATTGAC
1 ATTGAC
8287 AAAATTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 25 0.42
31 33 0.56
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (30 bp):
ATTGACCCACTAAAATAAAAGATTTATCAC
Found at i:8633 original size:11 final size:11
Alignment explanation
Indices: 8619--8656 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8609 ATTCATAACA
8619 AATTTATAATT
1 AATTTATAATT
8630 AATTTATAATT
1 AATTTATAATT
8641 -ATTTGATAATT
1 AATTT-ATAATT
*
8652 TATTT
1 AATTT
8657 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:12506 original size:24 final size:24
Alignment explanation
Indices: 12474--12526 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12464 ATTTAAAGAA
12474 GATCAACGTATGTGGAGGATTATT
1 GATCAACGTATGTGGAGGATTATT
* *
12498 GATCCACGTATGTGGGGGATTATT
1 GATCAACGTATGTGGAGGATTATT
12522 -ATCAA
1 GATCAA
12527 AGAAGATCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (24 bp):
GATCAACGTATGTGGAGGATTATT
Found at i:15341 original size:22 final size:23
Alignment explanation
Indices: 15298--15343 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
15288 ATTGAAAGAA
*
15298 GATCCACGTATGTGGAGGATTATT
1 GATCCACGTA-GTGAAGGATTATT
15322 GATCCACGTA-TGAAGGATTATT
1 GATCCACGTAGTGAAGGATTATT
15344 ATCAAAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
24 10 0.48
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (23 bp):
GATCCACGTAGTGAAGGATTATT
Found at i:15646 original size:62 final size:58
Alignment explanation
Indices: 15523--15636 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 58
15513 AAGACCCTCG
* *
15523 AATCAAATCAAACTCCTAAGTCATCAATTCAAGATCAAGTCATTCAACCCTTAAATCA
1 AATCAAATCAAACTCCAAAATCATCAATTCAAGATCAAGTCATTCAACCCTTAAATCA
15581 AATCAAATCAAACTCTCAAATTATCATCAAGTTCGAA-ATCAAGTCATTCAACCCTT
1 AATCAAATCAAACTC-CAAA--ATCATCAA-TTC-AAGATCAAGTCATTCAACCCTT
15637 GAAGTAAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
58 15 0.31
59 3 0.06
61 7 0.14
62 22 0.45
63 2 0.04
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.27
Consensus pattern (58 bp):
AATCAAATCAAACTCCAAAATCATCAATTCAAGATCAAGTCATTCAACCCTTAAATCA
Found at i:23165 original size:93 final size:92
Alignment explanation
Indices: 22986--23171 Score: 273
Period size: 93 Copynumber: 2.0 Consensus size: 92
22976 AACCTTCAAC
** * *
22986 TTTCTTAATTTTTTGAATGTAATTTTACATGGTGCCCACCTTGTTTGGTCCTAGATGCCCACCCT
1 TTTCTTAACATTTTGAATGTAATTTTACATGGTGCCCACCTTATTTGGTCATAGATGCCCACCCT
23051 CAAGTGATTAACTCGTAAAAATGTCCA
66 CAAGTGATTAACTCGTAAAAATGTCCA
* * *
23078 TTTCTTAACATTTTGTATGTAATTTTACATGGTGCCTACCCTTATTTGGTCATAGATGTCCACCC
1 TTTCTTAACATTTTGAATGTAATTTTACATGGTGCCCA-CCTTATTTGGTCATAGATGCCCACCC
* * *
23143 TCAATTGATTAACTTGTCAAAATGTCCA
65 TCAAGTGATTAACTCGTAAAAATGTCCA
23171 T
1 T
23172 GAACCATAAC
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
92 34 0.41
93 49 0.59
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (92 bp):
TTTCTTAACATTTTGAATGTAATTTTACATGGTGCCCACCTTATTTGGTCATAGATGCCCACCCT
CAAGTGATTAACTCGTAAAAATGTCCA
Found at i:28152 original size:26 final size:26
Alignment explanation
Indices: 28070--28152 Score: 70
Period size: 26 Copynumber: 3.4 Consensus size: 26
28060 CTTATATATT
*
28070 GTTCTTTGGTTAATAGAATGTAATCA
1 GTTCATTGGTTAATAGAATGTAATCA
* * * *
28096 GTTCATTGATT-GTTG--T-TTA-C-
1 GTTCATTGGTTAATAGAATGTAATCA
*
28116 GTTCTTTGGTTAATAGAATGTAATCA
1 GTTCATTGGTTAATAGAATGTAATCA
28142 GTTCATTGGTT
1 GTTCATTGGTT
28153 GTTTTTTCCT
Statistics
Matches: 40, Mismatches: 11, Indels: 12
0.63 0.17 0.19
Matches are distributed among these distances:
20 9 0.22
21 3 0.08
22 2 0.05
23 2 0.05
24 2 0.05
25 3 0.08
26 19 0.47
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.47
Consensus pattern (26 bp):
GTTCATTGGTTAATAGAATGTAATCA
Found at i:28536 original size:15 final size:15
Alignment explanation
Indices: 28516--28551 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28506 GCCAGTAATA
*
28516 CATCCCGCCCCGTCC
1 CATCCCGCCCCATCC
*
28531 CATCCCGTCCCATCC
1 CATCCCGCCCCATCC
28546 CATCCC
1 CATCCC
28552 CTCCAAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.64, G:0.08, T:0.17
Consensus pattern (15 bp):
CATCCCGCCCCATCC
Found at i:32073 original size:41 final size:41
Alignment explanation
Indices: 32028--32728 Score: 900
Period size: 41 Copynumber: 17.2 Consensus size: 41
32018 GAATGTGATA
*
32028 TTTACTTTTCCCAGTTTGCCCTTCCCAACCGGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* *
32069 TTTACTTTTTCCAGTTTGTCCTTCCCCA-CGAGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCG-GAAGGTGTTG
*
32110 TTTA-TTATTCCCAGTTTTCCCTTCCCCACCGGAAGGTGTTG
1 TTTACTT-TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
*
32151 TTTACTTTTCCCAGTTTGCCCTTCCCCTCCGGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* * *
32192 TTTACTTTTCCCAATTTGTCTTTCCCCA-CGAGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCG-GAAGGTGTTG
* * *
32233 TTTA-TTATTCCCACTTTGCCCTTCCCCACCGAAAGTTGTTG
1 TTTACTT-TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* *
32274 TTCACTTTTCCCAGTTTGCCCTTCCCCACCAGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* *
32315 TTT--TTATTCCCAGTTTGCCCTTCCCCACCAGAAGGTGTAG
1 TTTACTT-TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
*
32355 TTTACTTTTCCCAGTTTGCCCTTCCCCACTGGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* * * * *
32396 TTTAATATTCTCAGTTTGCCCTTCTCCACTGGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* * ** ** ** *
32437 TTTACTTTTCCTAGTCTGTACTTCCTTAATGGAAAGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
*
32478 TTTAC-TTTCCCAGTTTGCCCTTCCCCACTGGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
*
32518 TTTA-TTATT-CCAGTTTGCCCTTCCCCATCGGAAGGTGTTG
1 TTTACTT-TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
** *
32558 TTTACTTTTCCCAGTTTGCCCTTCCCCAATGGAAAGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* * * *
32599 TTTACTTTTCCCAGCTTGCCTTTCCTCACTGGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
* *
32640 TTTA-TTATTCCTAGTTTGCCCTTCACCACCGGAAGGTGTTG
1 TTTACTT-TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
32681 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
32722 TTTACTT
1 TTTACTT
32729 ATCTTATTTC
Statistics
Matches: 574, Mismatches: 69, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.00
40 113 0.20
41 447 0.78
42 12 0.02
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (41 bp):
TTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG
Found at i:35184 original size:22 final size:20
Alignment explanation
Indices: 35159--35202 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
35149 AATTTATAAT
35159 TTTGCCTTCTGAAATTGCTGCC
1 TTTGCCTTC--AAATTGCTGCC
* *
35181 TTTGGCTTCAAATTGCTTCC
1 TTTGCCTTCAAATTGCTGCC
35201 TT
1 TT
35203 GGAAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.45
Consensus pattern (20 bp):
TTTGCCTTCAAATTGCTGCC
Found at i:36476 original size:2 final size:2
Alignment explanation
Indices: 36469--36514 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
36459 CAAAAGGTCC
*
36469 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36510 TA TA T
1 TA TA T
36515 CTTTAAACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37159 original size:8 final size:8
Alignment explanation
Indices: 37146--37172 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
37136 TACTGATAAC
37146 ATTGCTTT
1 ATTGCTTT
37154 ATTGCTTT
1 ATTGCTTT
37162 ATTGCTTT
1 ATTGCTTT
37170 ATT
1 ATT
37173 CTCTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.63
Consensus pattern (8 bp):
ATTGCTTT
Found at i:39552 original size:11 final size:11
Alignment explanation
Indices: 39527--39559 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39517 TCACAACCAA
39527 ACAAAAGCA-T
1 ACAAAAGCATT
39537 ACAAAAGCATT
1 ACAAAAGCATT
*
39548 ACAAATGCATT
1 ACAAAAGCATT
39559 A
1 A
39560 GTTTATTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (11 bp):
ACAAAAGCATT
Found at i:41004 original size:33 final size:33
Alignment explanation
Indices: 40966--41060 Score: 145
Period size: 33 Copynumber: 2.9 Consensus size: 33
40956 CTTGGCGACT
*
40966 CAATAATTTTAGCATCAATCTAAGCTGATAACC
1 CAATAATTTTAGCATCGATCTAAGCTGATAACC
* * *
40999 CAATAATTTTAACATCGATTTGAGCTGATAACC
1 CAATAATTTTAGCATCGATCTAAGCTGATAACC
*
41032 CAATAATTTCAGCATCGATCTAAGCTGAT
1 CAATAATTTTAGCATCGATCTAAGCTGAT
41061 CGTCTTTGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATAATTTTAGCATCGATCTAAGCTGATAACC
Found at i:48396 original size:26 final size:26
Alignment explanation
Indices: 48325--48407 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 26
48315 CTTACTCTCC
48325 TTTTTACTGATTACCATTTTTACTTTTTTT
1 TTTTTACTGATTACCATTTTTAC----TTT
* * *
48355 TTTTATATTGAATACCCTTTTTACTTT
1 TTTT-TACTGATTACCATTTTTACTTT
*
48382 TTTTTACTGATTACCATTTTCACTTT
1 TTTTTACTGATTACCATTTTTACTTT
48408 ACTGATTACT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
26 18 0.40
27 7 0.16
30 4 0.09
31 16 0.36
ACGTcount: A:0.19, C:0.16, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTTTACTGATTACCATTTTTACTTT
Found at i:48408 original size:21 final size:21
Alignment explanation
Indices: 48384--48430 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
48374 TTTACTTTTT
*
48384 TTTACTGATTACCATTTTCAC
1 TTTACTGATTACCATTTACAC
* *
48405 TTTACTGATTACTATTTACTC
1 TTTACTGATTACCATTTACAC
48426 TTTAC
1 TTTAC
48431 CATTTTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTACTGATTACCATTTACAC
Found at i:48409 original size:31 final size:30
Alignment explanation
Indices: 48325--48410 Score: 74
Period size: 31 Copynumber: 2.9 Consensus size: 30
48315 CTTACTCTCC
*
48325 TTTTTACTGATTACCATTTTTACTTT-TTTT
1 TTTTTACTGATTACCA-TTTTACTTTACTTT
* * *
48355 TTTTATATTGAATACC--CTT--TTTACTTT
1 TTTT-TACTGATTACCATTTTACTTTACTTT
48382 TTTTTACTGATTACCATTTTCACTTTACT
1 TTTTTACTGATTACCATTTT-ACTTTACT
48411 GATTACTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
26 12 0.29
27 7 0.17
28 4 0.10
30 4 0.10
31 15 0.36
ACGTcount: A:0.20, C:0.16, G:0.03, T:0.60
Consensus pattern (30 bp):
TTTTTACTGATTACCATTTTACTTTACTTT
Found at i:48452 original size:36 final size:36
Alignment explanation
Indices: 48392--48708 Score: 383
Period size: 36 Copynumber: 8.8 Consensus size: 36
48382 TTTTTACTGA
* * *
48392 TTACCATTTT-CACTTTACTGATTACTATTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* * *
48427 TTACCATTTTACTTTTTACGGATTACTCTTTTTCTTT
1 TTACCATTTTACTCTTTACTGATTACTC-TTTACTTT
* *
48464 TTACCATTTTACTCTTTAGTGGTTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* **
48500 TTACCATTTTACTCTTTACTGATTGCTCTTTACTGA
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
48536 TTA-C-TCTTTACTCTTTACCAT-TTTACTCTTTACTTT
1 TTACCAT-TTTACTCTTTA-C-TGATTACTCTTTACTTT
*
48572 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
48608 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* * * * *
48644 CTACTATTTTACTGTTTACTGATCAC-CATTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
48679 TTACCATTTTACTCTTTACTGATTAATCTT
1 TTACCATTTTACTCTTTACTGATTACTCTT
48709 ATTTCTTTAC
Statistics
Matches: 238, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.00
35 52 0.22
36 141 0.59
37 43 0.18
38 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (36 bp):
TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
Found at i:48664 original size:7 final size:7
Alignment explanation
Indices: 48471--48663 Score: 108
Period size: 7 Copynumber: 26.9 Consensus size: 7
48461 TTTTTACCAT
48471 TTTACTC
1 TTTACTC
* *
48478 TTTAGTG
1 TTTACTC
*
48485 GTTACTC
1 TTTACTC
*
48492 TTTACTT
1 TTTACTC
48499 TTTAC-C
1 TTTACTC
48505 ATTTTACTC
1 --TTTACTC
*
48514 TTTACTG
1 TTTACTC
* *
48521 ATTGCTC
1 TTTACTC
*
48528 TTTACTG
1 TTTACTC
*
48535 ATTACTC
1 TTTACTC
48542 TTTACTC
1 TTTACTC
48549 TTTAC-C
1 TTTACTC
48555 ATTTTACTC
1 --TTTACTC
*
48564 TTTACTT
1 TTTACTC
48571 TTTAC-C
1 TTTACTC
48577 ATTTTACTC
1 --TTTACTC
*
48586 TTTACTG
1 TTTACTC
*
48593 ATTACTC
1 TTTACTC
48600 TTTACTC
1 TTTACTC
48607 TTTAC-C
1 TTTACTC
*
48613 ATTTTACTT
1 --TTTACTC
*
48622 TTTACTG
1 TTTACTC
*
48629 ATTACTC
1 TTTACTC
48636 TTTACT-
1 TTTACTC
*
48642 TTCTACTAT
1 TT-TACT-C
*
48651 TTTACTG
1 TTTACTC
48658 TTTACT
1 TTTACT
48664 GATCACCATT
Statistics
Matches: 141, Mismatches: 30, Indels: 30
0.70 0.15 0.15
Matches are distributed among these distances:
6 4 0.03
7 108 0.77
8 24 0.17
9 5 0.04
ACGTcount: A:0.18, C:0.22, G:0.05, T:0.55
Consensus pattern (7 bp):
TTTACTC
Found at i:48682 original size:7 final size:7
Alignment explanation
Indices: 48413--48663 Score: 97
Period size: 7 Copynumber: 34.7 Consensus size: 7
48403 ACTTTACTGA
*
48413 TTACTAT
1 TTACTTT
*
48420 TTACTCT
1 TTACTTT
*
48427 TTACCATT
1 TTA-CTTT
48435 TTACTTT
1 TTACTTT
***
48442 TTACGGA
1 TTACTTT
48449 TTACTCTT
1 TTACT-TT
*
48457 TTTCTTT
1 TTACTTT
*
48464 TTACCATT
1 TTA-CTTT
*
48472 TTACTCT
1 TTACTTT
* **
48479 TTAGTGG
1 TTACTTT
*
48486 TTACTCT
1 TTACTTT
48493 TTACTTT
1 TTACTTT
*
48500 TTACCATT
1 TTA-CTTT
*
48508 TTACTCT
1 TTACTTT
**
48515 TTACTGA
1 TTACTTT
* *
48522 TTGCTCT
1 TTACTTT
**
48529 TTACTGA
1 TTACTTT
*
48536 TTACTCT
1 TTACTTT
*
48543 TTACTCT
1 TTACTTT
*
48550 TTACCATT
1 TTA-CTTT
*
48558 TTACTCT
1 TTACTTT
48565 TTACTTT
1 TTACTTT
*
48572 TTACCATT
1 TTA-CTTT
*
48580 TTACTCT
1 TTACTTT
**
48587 TTACTGA
1 TTACTTT
*
48594 TTACTCT
1 TTACTTT
*
48601 TTACTCT
1 TTACTTT
*
48608 TTACCATT
1 TTA-CTTT
48616 TTACTTT
1 TTACTTT
**
48623 TTACTGA
1 TTACTTT
*
48630 TTACTCT
1 TTACTTT
48637 TTACTTT
1 TTACTTT
*
48644 CTACTATT
1 TTACT-TT
*
48652 TTACTGT
1 TTACTTT
48659 TTACT
1 TTACT
48664 GATCACCATT
Statistics
Matches: 178, Mismatches: 58, Indels: 16
0.71 0.23 0.06
Matches are distributed among these distances:
7 135 0.76
8 43 0.24
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (7 bp):
TTACTTT
Found at i:50819 original size:19 final size:18
Alignment explanation
Indices: 50786--50822 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
50776 TTGAAATAAT
50786 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
50804 TCTTCAAATTATCTTCAAG
1 TCTTC-AATAATCTTCAAG
50823 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:63133 original size:31 final size:31
Alignment explanation
Indices: 63115--63177 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
63105 CAAAACACAT
*
63115 TAAAATGTTAAGGTCCCAAAAAAAAGTAAGC
1 TAAAATGTTAAGGTCCCAAAAAAAAGCAAGC
* *
63146 TAAAATGTTAAGGTCCCAAAAGAAAGTAAGC
1 TAAAATGTTAAGGTCCCAAAAAAAAGCAAGC
63177 T
1 T
63178 TAAGGAGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (31 bp):
TAAAATGTTAAGGTCCCAAAAAAAAGCAAGC
Found at i:63576 original size:3 final size:3
Alignment explanation
Indices: 63568--63596 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
63558 TAAAATTCCC
63568 CTT CTT CTT CTT CTT CTT CTT CTT -TT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
63597 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:63728 original size:48 final size:47
Alignment explanation
Indices: 63667--63949 Score: 277
Period size: 48 Copynumber: 6.0 Consensus size: 47
63657 CCGAGGTCTA
* *
63667 AAATTG-AAGACTCACGTGGAAGCGAGAAAAGACCAACCTTGGTCA-A
1 AAATTGTAA-ACTCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACT
* ** * *
63713 AGACATTGTAAACTCACATGGAAATGAGAAAAGGCCAACTTTGGTCACC
1 A-A-ATTGTAAACTCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACT
* ** *
63762 AAATT-TAAACTCACATGGAAATGAGGAAAGACCAACTTTGGTCACT
1 AAATTGTAAACTCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACT
* * *
63808 AAATTGTAGACTCGCGTGGAAGCGAGAAAAACACCAACTTTGGTCACT
1 AAATTGTAAACTCACGTGGAAGCGAG-AAAAGACCAACTTTGGTCACT
*** *
63856 AAATTGCCGACTCGCGTGGAAGCGAGAAAAAGACCAACTTTGGTCACT
1 AAATTGTAAACTCACGTGGAAGCGAG-AAAAGACCAACTTTGGTCACT
** * * *
63904 AAATT-TCCGACTCGCGTGGAAGTGAGAAAAAACCAACTTTGGTCAC
1 AAATTGT-AAACTCACGTGGAAGCGAGAAAAGACCAACTTTGGTCAC
63950 AGAAAACTGC
Statistics
Matches: 208, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
46 44 0.21
47 38 0.18
48 123 0.59
49 3 0.01
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (47 bp):
AAATTGTAAACTCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACT
Found at i:64219 original size:88 final size:87
Alignment explanation
Indices: 64105--64267 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 87
64095 CCCGGAGGCA
* *
64105 ATCAGAATTGTGGCCCGGAGGCTTCTGATTTCGTGCCTAGAGGCT-GTCAAAATTACTACCCGGA
1 ATCAGAATTGTGGCCCGGAGGCTTCTGATTT-GTGCCCAGAGG-TGGCCAAAATTACTACCCGGA
64169 GGTTTCTGACATCGTTTTGAAATT
64 GGTTTCTGACATCGTTTTGAAATT
* * * * * *
64193 ATCAGAATTGCT-GTCCGGAGGCTTCTGATTTTTGCCCGGAGGTGGCCAGAATTGCTACCTGGAG
1 ATCAGAATTG-TGGCCCGGAGGCTTCTGATTTGTGCCCAGAGGTGGCCAAAATTACTACCCGGAG
64257 GTTTCTGACAT
65 GTTTCTGACAT
64268 TGTGCCCGGA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
86 1 0.02
87 35 0.54
88 28 0.43
89 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (87 bp):
ATCAGAATTGTGGCCCGGAGGCTTCTGATTTGTGCCCAGAGGTGGCCAAAATTACTACCCGGAGG
TTTCTGACATCGTTTTGAAATT
Found at i:64257 original size:44 final size:45
Alignment explanation
Indices: 64195--64280 Score: 113
Period size: 44 Copynumber: 1.9 Consensus size: 45
64185 TTGAAATTAT
* * *
64195 CAGAATTGCTGTCCGGAGGCTTCTGA-TTTTTGCCCGGAGGTGGC
1 CAGAATTGCTGACCGGAGGCTTCTGACATTGTGCCCGGAGGTGGC
*
64239 CAGAATTGCT-ACCTGGAGGTTTCTGACATTGTGCCCGGAGGT
1 CAGAATTGCTGACC-GGAGGCTTCTGACATTGTGCCCGGAGGT
64281 CTTATAACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 2 0.06
44 21 0.58
45 13 0.36
ACGTcount: A:0.16, C:0.22, G:0.33, T:0.29
Consensus pattern (45 bp):
CAGAATTGCTGACCGGAGGCTTCTGACATTGTGCCCGGAGGTGGC
Found at i:65186 original size:10 final size:10
Alignment explanation
Indices: 65171--65199 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
65161 TGATCATCTA
65171 AACCTCCTTC
1 AACCTCCTTC
65181 AACCTCCTTC
1 AACCTCCTTC
65191 AACCTCCTT
1 AACCTCCTT
65200 TTGCTTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.48, G:0.00, T:0.31
Consensus pattern (10 bp):
AACCTCCTTC
Found at i:66102 original size:87 final size:87
Alignment explanation
Indices: 65956--66135 Score: 315
Period size: 87 Copynumber: 2.1 Consensus size: 87
65946 TTTTCATTCA
* * *
65956 TTTTTTCTTGGTTGCTTCACCATGCACTTGCATTTGAAAACTTTTGAAAACCAATTTTATCTAAA
1 TTTTTTATTGGTTGCTTCACCACGCACTTGCATTCGAAAACTTTTGAAAACCAATTTTATCTAAA
66021 AACCTTTTTGAGAAAAACATTT
66 AACCTTTTTGAGAAAAACATTT
*
66043 TTTTTTATTGGTTGCTTCACCACGCACTTGCATTCGAAAACTTTTGGAAACCAATTTTATCTAAA
1 TTTTTTATTGGTTGCTTCACCACGCACTTGCATTCGAAAACTTTTGAAAACCAATTTTATCTAAA
*
66108 AATCTTTTTGAGAAAAACATTT
66 AACCTTTTTGAGAAAAACATTT
66130 TTTTTT
1 TTTTTT
66136 TTGCAAAAAC
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (87 bp):
TTTTTTATTGGTTGCTTCACCACGCACTTGCATTCGAAAACTTTTGAAAACCAATTTTATCTAAA
AACCTTTTTGAGAAAAACATTT
Found at i:67303 original size:3 final size:3
Alignment explanation
Indices: 67295--67349 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
67285 GTCCACTTTT
* *
67295 TTA TTA TTA TTA TTA TT- TTA TTA TTC TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
67342 TTA TTA TT
1 TTA TTA TT
67350 TTAAAACTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:70500 original size:28 final size:27
Alignment explanation
Indices: 70465--70547 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 27
70455 CTTACTCTCC
70465 TTTTTACTCATTACCATTTTTACTTTT
1 TTTTTACTCATTACCATTTTTACTTTT
* *
70492 TTTTATACTGATTACCCTTTTTTACTCTTT
1 TTTT-TACTCATTA-CCATTTTTACT-TTT
*
70522 TTTTTAC-CGATTACCATTTTCACTTT
1 TTTTTACTC-ATTACCATTTTTACTTT
70548 ACTGATTACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
27 6 0.13
28 17 0.36
29 17 0.36
30 7 0.15
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTTACTCATTACCATTTTTACTTTT
Found at i:70523 original size:29 final size:28
Alignment explanation
Indices: 70456--70541 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
70446 GCCTCTATTC
* * *
70456 TTACTCTCCTTTTTACTCATTA-CCATTT
1 TTACTCT-TTTTTTACTGATTACCCTTTT
*
70484 TTACTTTTTTTTATACTGATTACCCTTTT
1 TTACTCTTTTTT-TACTGATTACCCTTTT
* *
70513 TTACTCTTTTTTTTACCGATTACCATTTT
1 TTACTC-TTTTTTTACTGATTACCCTTTT
70542 CACTTTACTG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.08
28 14 0.29
29 24 0.50
30 6 0.12
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.58
Consensus pattern (28 bp):
TTACTCTTTTTTTACTGATTACCCTTTT
Found at i:70554 original size:21 final size:21
Alignment explanation
Indices: 70524--70571 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
70514 TACTCTTTTT
*
70524 TTTACCGATTACCATTTTCAC
1 TTTACCGATTACCATTTACAC
* * *
70545 TTTACTGATTACTATTTACTC
1 TTTACCGATTACCATTTACAC
70566 TTTACC
1 TTTACC
70572 ATTTTACTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.04, T:0.48
Consensus pattern (21 bp):
TTTACCGATTACCATTTACAC
Found at i:70563 original size:7 final size:7
Alignment explanation
Indices: 70553--70815 Score: 59
Period size: 7 Copynumber: 36.3 Consensus size: 7
70543 ACTTTACTGA
70553 TTACTAT
1 TTACTAT
*
70560 TTACTCT
1 TTACTAT
*
70567 TTACCATT
1 TTACTA-T
*
70575 TTACTTT
1 TTACTAT
70582 TTACTGA-
1 TTACT-AT
*
70589 TTACTCTT
1 TTACT-AT
* *
70597 TTTCTTT
1 TTACTAT
*
70604 TTACCATT
1 TTACTA-T
*
70612 TTACTCT
1 TTACTAT
**
70619 TTACTGG
1 TTACTAT
**
70626 TTACCCT
1 TTACTAT
*
70633 TTACTCT
1 TTACTAT
*
70640 TTACCATT
1 TTACTA-T
*
70648 TTACTTT
1 TTACTAT
*
70655 TTATTGA-
1 TTACT-AT
*
70662 TTACTCT
1 TTACTAT
*
70669 TTACTTT
1 TTACTAT
*
70676 TTACCATT
1 TTACTA-T
*
70684 TTACTCT
1 TTACTAT
70691 ATTACTGA-
1 -TTACT-AT
*
70699 TTACTCT
1 TTACTAT
*
70706 TTACTCT
1 TTACTAT
*
70713 TTACCATT
1 TTACTA-T
*
70721 TTACTCT
1 TTACTAT
*
70728 TTACTTT
1 TTACTAT
*
70735 TTACCATT
1 TTACTA-T
*
70743 TTACTCT
1 TTACTAT
70750 TTACTGA-
1 TTACT-AT
**
70757 TTACGCT
1 TTACTAT
*
70764 TTACTCT
1 TTACTAT
*
70771 TTACCATT
1 TTACTA-T
*
70779 TTACTTT
1 TTACTAT
70786 TTACTGA-
1 TTACT-AT
*
70793 TTACTCT
1 TTACTAT
*
70800 TTACTTT
1 TTACTAT
70807 TTACTAT
1 TTACTAT
70814 TT
1 TT
70816 TATTGTTTAC
Statistics
Matches: 182, Mismatches: 56, Indels: 36
0.66 0.20 0.13
Matches are distributed among these distances:
7 138 0.76
8 44 0.24
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTAT
Found at i:70584 original size:22 final size:20
Alignment explanation
Indices: 70553--70861 Score: 86
Period size: 22 Copynumber: 14.9 Consensus size: 20
70543 ACTTTACTGA
*
70553 TTACTATTTACTCTTTACCATT
1 TTACTTTTTACTCTTTA-C-TT
**
70575 TTACTTTTTACTGATTACTCTT
1 TTACTTTTTACTCTTTA--CTT
*
70597 TTTCTTTTTAC-CATTTTACTCT
1 TTACTTTTTACTC--TTTACT-T
** *
70619 TTACTGGTTACCCTTTACTCT
1 TTACTTTTTACTCTTTACT-T
* *
70640 TTACCATTTTACTTTTTA--T
1 TTA-CTTTTTACTCTTTACTT
*
70659 TGA---TT-ACTCTTTACTTT
1 TTACTTTTTACTCTTTAC-TT
* *
70676 TTACCATTTTACTCTATTACTGA
1 TTA-CTTTTTACTCT-TTACT-T
*
70699 TTACTCTTTACTCTTTAC--
1 TTACTTTTTACTCTTTACTT
*
70717 ---CATTTTACTCTTTACTTT
1 TTACTTTTTACTCTTTAC-TT
* *
70735 TTACCATTTTACTCTTTACTGA
1 TTA-CTTTTTACTCTTTACT-T
**
70757 TTACGCTTTACTCTTTACCATT
1 TTACTTTTTACTCTTTA-C-TT
**
70779 TTACTTTTTACTGATTACTCT
1 TTACTTTTTACTCTTTACT-T
* *
70800 TTACTTTTTACTATTTTATTGT
1 TTACTTTTTACT-CTTTACT-T
** * *
70822 TTACTGATCAC-CATTACTTT
1 TTACTTTTTACTCTTTAC-TT
70842 TTACTATTTTACTCTTTACT
1 TTACT-TTTTACTCTTTACT
70862 GATTACTCTT
Statistics
Matches: 211, Mismatches: 45, Indels: 63
0.66 0.14 0.20
Matches are distributed among these distances:
14 7 0.03
15 15 0.07
17 3 0.01
19 3 0.01
20 10 0.05
21 51 0.24
22 109 0.52
23 13 0.06
ACGTcount: A:0.19, C:0.21, G:0.03, T:0.56
Consensus pattern (20 bp):
TTACTTTTTACTCTTTACTT
Found at i:70636 original size:73 final size:72
Alignment explanation
Indices: 70532--70732 Score: 314
Period size: 73 Copynumber: 2.8 Consensus size: 72
70522 TTTTTACCGA
* *
70532 TTACCATTTT-CACTTTACTGATTACTATTTACTCTTTACCATTTTACTTTTTACTGATTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCTTTACCATTTTACTTTTTACTGATTACTC-
*
70596 TTTTCTTT
65 TTTACTTT
* * *
70604 TTACCATTTTACTCTTTACTGGTTACCCTTTACTCTTTACCATTTTACTTTTTATTGATTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCTTTACCATTTTACTTTTTACTGATTACTCT
70669 TTACTTT
66 TTACTTT
*
70676 TTACCATTTTACTCTATTACTGATTACTCTTTACTCTTTACCATTTTACTCTTTACT
1 TTACCATTTTACTCT-TTACTGATTACTCTTTACTCTTTACCATTTTACTTTTTACT
70733 TTTTACCATT
Statistics
Matches: 117, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
72 32 0.27
73 85 0.73
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.55
Consensus pattern (72 bp):
TTACCATTTTACTCTTTACTGATTACTCTTTACTCTTTACCATTTTACTTTTTACTGATTACTCT
TTACTTT
Found at i:70723 original size:15 final size:14
Alignment explanation
Indices: 70559--70811 Score: 87
Period size: 14 Copynumber: 17.4 Consensus size: 14
70549 CTGATTACTA
70559 TTTACTCTTTACCAT
1 TTTACTCTTTACC-T
*
70574 TTTACTTTTTA-CT
1 TTTACTCTTTACCT
* * *
70587 GATTACTCTTTTTCTT
1 -TTTACTC-TTTACCT
70603 TTTAC-CATTTTA-CT
1 TTTACTC--TTTACCT
** *
70617 CTTTACTGGTTACCC
1 -TTTACTCTTTACCT
70632 TTTACTCTTTACCAT
1 TTTACTCTTTACC-T
*
70647 TTTACTTTTTA--T
1 TTTACTCTTTACCT
*
70659 TGATTACTCTTTACTT
1 T--TTACTCTTTACCT
70675 TTTAC-CATTTTACTCT
1 TTTACTC--TTTAC-CT
* **
70691 ATTACTGATTA-CT
1 TTTACTCTTTACCT
70704 CTTTACTCTTTACCAT
1 -TTTACTCTTTACC-T
*
70720 TTTACTCTTTACTT
1 TTTACTCTTTACCT
70734 TTTAC-CATTTTA-CT
1 TTTACTC--TTTACCT
**
70748 CTTTACTGATTACGC-
1 -TTTACTCTTTAC-CT
70763 TTTACTCTTTACCAT
1 TTTACTCTTTACC-T
*
70778 TTTACTTTTTA-CT
1 TTTACTCTTTACCT
* *
70791 GATTACTCTTTACTT
1 -TTTACTCTTTACCT
70806 TTTACT
1 TTTACT
70812 ATTTTATTGT
Statistics
Matches: 175, Mismatches: 34, Indels: 59
0.65 0.13 0.22
Matches are distributed among these distances:
12 2 0.01
13 7 0.04
14 78 0.45
15 78 0.45
16 10 0.06
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTACTCTTTACCT
Found at i:70766 original size:36 final size:36
Alignment explanation
Indices: 70721--70871 Score: 214
Period size: 36 Copynumber: 4.2 Consensus size: 36
70711 CTTTACCATT
70721 TTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
* * *
70757 TTACGCTTTACTCTTTACCATTTTACTTTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
* * *
70793 TTACTCTTTACTTTTTACTATTTTATTGTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
* * *
70829 TCAC-CATTACTTTTTACTATTTTACTCTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
70864 TTACTCTT
1 TTACTCTT
70872 ATTTCTTTAC
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 31 0.31
36 69 0.69
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.56
Consensus pattern (36 bp):
TTACTCTTTACTTTTTACCATTTTACTCTTTACTGA
Found at i:70766 original size:58 final size:59
Alignment explanation
Indices: 70662--70790 Score: 233
Period size: 58 Copynumber: 2.2 Consensus size: 59
70652 TTTTTATTGA
*
70662 TTACTCTTTACTTTTTACCATTTTACTCTATTACTGATTACTCTTTACTCTTTACCATT
1 TTACTCTTTACTTTTTACCATTTTACTCTATTACTGATTACGCTTTACTCTTTACCATT
70721 TTACTCTTTACTTTTTACCATTTTACTCT-TTACTGATTACGCTTTACTCTTTACCATT
1 TTACTCTTTACTTTTTACCATTTTACTCTATTACTGATTACGCTTTACTCTTTACCATT
*
70779 TTACTTTTTACT
1 TTACTCTTTACT
70791 GATTACTCTT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 39 0.57
59 29 0.43
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.55
Consensus pattern (59 bp):
TTACTCTTTACTTTTTACCATTTTACTCTATTACTGATTACGCTTTACTCTTTACCATT
Found at i:70880 original size:21 final size:22
Alignment explanation
Indices: 70854--70958 Score: 98
Period size: 21 Copynumber: 5.0 Consensus size: 22
70844 ACTATTTTAC
70854 TCTTTACTGATTACTC-TTA-TT
1 TCTTTACTGATTAC-CATTACTT
70875 TCTTTACTGATTACCATTACTT
1 TCTTTACTGATTACCATTACTT
*
70897 T-TTTACTGATTACCATTAC-C
1 TCTTTACTGATTACCATTACTT
*
70917 T-TTTACTGAATACCATTTTAC-T
1 TCTTTACTGATTACCA--TTACTT
* *
70939 T-TTTATTGATTGCCATTACT
1 TCTTTACTGATTACCATTACT
70959 CTTTAACTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
20 19 0.26
21 35 0.48
22 19 0.26
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (22 bp):
TCTTTACTGATTACCATTACTT
Found at i:70881 original size:56 final size:56
Alignment explanation
Indices: 70779--70909 Score: 167
Period size: 56 Copynumber: 2.3 Consensus size: 56
70769 CTTTACCATT
** * *
70779 TTACTTTTTACTGATTACTCTTTACTTTTTACTATTTTATTGTTTACTGATCACCA
1 TTACTTTTTACTGATTACTCTTTACTGATTACTATTATATTCTTTACTGATCACCA
* *
70835 TTACTTTTTACT-ATTTTACTCTTTACTGATTACTCTTAT-TTCTTTACTGATTACCA
1 TTACTTTTTACTGA--TTACTCTTTACTGATTACTATTATATTCTTTACTGATCACCA
70891 TTACTTTTTTACTGATTAC
1 TTAC-TTTTTACTGATTAC
70910 CATTACCTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 1 0.02
56 35 0.54
57 28 0.43
58 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (56 bp):
TTACTTTTTACTGATTACTCTTTACTGATTACTATTATATTCTTTACTGATCACCA
Found at i:70942 original size:42 final size:42
Alignment explanation
Indices: 70847--70971 Score: 121
Period size: 42 Copynumber: 2.9 Consensus size: 42
70837 ACTTTTTACT
* ** *
70847 ATTTTACTCTTTACTGATTACTC-TTATTTCTTTACTGATTACC
1 ATTTTACTTTTTACTGATTAC-CATTACCT-TTTACTGAATACC
70890 A--TTACTTTTTTACTGATTACCATTACCTTTTACTGAATACC
1 ATTTTAC-TTTTTACTGATTACCATTACCTTTTACTGAATACC
* * *
70931 ATTTTACTTTTTATTGATTGCCATTACTCTTTAACTTGAAT
1 ATTTTACTTTTTACTGATTACCATTAC-CTTTTAC-TGAAT
70972 TACTGATTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
41 18 0.26
42 35 0.51
43 11 0.16
44 5 0.07
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (42 bp):
ATTTTACTTTTTACTGATTACCATTACCTTTTACTGAATACC
Found at i:76747 original size:20 final size:20
Alignment explanation
Indices: 76722--76760 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
76712 AAGGGAGCAT
76722 AAGGGGAGAAGAGTCACATC
1 AAGGGGAGAAGAGTCACATC
76742 AAGGGGAGAAGAGTCACAT
1 AAGGGGAGAAGAGTCACAT
76761 ACCTTGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.36, T:0.10
Consensus pattern (20 bp):
AAGGGGAGAAGAGTCACATC
Found at i:78349 original size:35 final size:35
Alignment explanation
Indices: 78302--78614 Score: 368
Period size: 35 Copynumber: 8.9 Consensus size: 35
78292 GTGAATCAGT
* **
78302 AATAAGCAACTTAATTCAGGGTAATTAAGCAAGTC
1 AATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
**
78337 GGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
* *
78372 AGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTT
1 AATAATCAAC-TTAATTCAGGGTAATTAAGTGAGTC
78408 AATAAGT-AACTTAATTCAGGGTAATTAAGT-AGTTC
1 AATAA-TCAACTTAATTCAGGGTAATTAAGTGAG-TC
* *
78443 AATGAGT-AACTTAATTCAGGTTAATTAAGTGAGTC
1 AAT-AATCAACTTAATTCAGGGTAATTAAGTGAGTC
**
78478 GGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTC
1 AATAATCAAC-TTAATTCAGGGTAATTAAGTGAGTC
* * *
78514 AGTAATCAACTTTAATTCAGGGTAACTAAGTGAGTT
1 AATAATCAAC-TTAATTCAGGGTAATTAAGTGAGTC
*
78550 AATGAGT-AACTTAATTCAGGGTAATTAAGT-AGTTC
1 AAT-AATCAACTTAATTCAGGGTAATTAAGTGAG-TC
78585 AATAAGT-AACTTAATTCAGGGTAATTAAGT
1 AATAA-TCAACTTAATTCAGGGTAATTAAGT
78615 CTGGTAAGAA
Statistics
Matches: 245, Mismatches: 23, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
34 7 0.03
35 139 0.57
36 96 0.39
37 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (35 bp):
AATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
Found at i:78486 original size:106 final size:106
Alignment explanation
Indices: 78301--78614 Score: 417
Period size: 106 Copynumber: 3.0 Consensus size: 106
78291 GGTGAATCAG
* * ** *
78301 TAATAAGCAACTTAATTCAGGGTAATTAAGCAAG-TCGGT-AATCAACTTAATTCAGGGTAATTA
1 TAATAAGTAACTTAATTCAGGGTAATTAAG-TAGTTCAATGAGT-AACTTAATTCAGGGTAATTA
78364 AGTGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGT
64 AGTGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGT
*
78407 TAATAAGTAACTTAATTCAGGGTAATTAAGTAGTTCAATGAGTAACTTAATTCAGGTTAATTAAG
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTAGTTCAATGAGTAACTTAATTCAGGGTAATTAAG
*
78472 TGAGTCGGTAATCAACTTTAATTCAGGGTAATTAAGTGAGT
66 TGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGT
* * *
78513 CAGTAA-TCAACTTTAATTCAGGGTAACTAAGTGAGTT-AATGAGTAACTTAATTCAGGGTAATT
1 TAATAAGT-AAC-TTAATTCAGGGTAATTAAGT-AGTTCAATGAGTAACTTAATTCAGGGTAATT
*
78576 AAGT-AGTTCAATAAGT-AAC-TTAATTCAGGGTAATTAAGT
63 AAGTGAG-TCAGTAA-TCAACTTTAATTCAGGGTAATTAAGT
78615 CTGGTAAGAA
Statistics
Matches: 188, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
105 3 0.02
106 122 0.65
107 58 0.31
108 5 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (106 bp):
TAATAAGTAACTTAATTCAGGGTAATTAAGTAGTTCAATGAGTAACTTAATTCAGGGTAATTAAG
TGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGT
Found at i:78503 original size:20 final size:20
Alignment explanation
Indices: 78478--78538 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
78468 TAAGTGAGTC
78478 GGTAATCAACTTTAATTCAG
1 GGTAATCAACTTTAATTCAG
* * * *
78498 GGTAATTAA--GTGAGTCA-
1 GGTAATCAACTTTAATTCAG
78515 -GTAATCAACTTTAATTCAG
1 GGTAATCAACTTTAATTCAG
78534 GGTAA
1 GGTAA
78539 CTAAGTGAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
16 7 0.24
18 10 0.34
20 12 0.41
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (20 bp):
GGTAATCAACTTTAATTCAG
Found at i:78564 original size:142 final size:141
Alignment explanation
Indices: 78302--78614 Score: 554
Period size: 142 Copynumber: 2.2 Consensus size: 141
78292 GTGAATCAGT
* *
78302 AATAAGCAACTTAATTCAGGGTAATTAAGCAAGTCGGTAATCAACTTAATTCAGGGTAATTAAGT
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTCGGTAATCAACTTAATTCAGGGTAATTAAGT
*
78367 GAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTTAATAAGTAACTTAATTCAGGGTAA
66 GAGTCAGTAATCAACTTTAATTCAGGGTAACTAAGTGAGTTAATAAGTAACTTAATTCAGGGTAA
78432 TTAAGTAGTTC
131 TTAAGTAGTTC
* * *
78443 AATGAGTAACTTAATTCAGGTTAATTAAGTGAGTCGGTAATCAACTTTAATTCAGGGTAATTAAG
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTCGGTAATCAAC-TTAATTCAGGGTAATTAAG
*
78508 TGAGTCAGTAATCAACTTTAATTCAGGGTAACTAAGTGAGTTAATGAGTAACTTAATTCAGGGTA
65 TGAGTCAGTAATCAACTTTAATTCAGGGTAACTAAGTGAGTTAATAAGTAACTTAATTCAGGGTA
78573 ATTAAGTAGTTC
130 ATTAAGTAGTTC
78585 AATAAGTAACTTAATTCAGGGTAATTAAGT
1 AATAAGTAACTTAATTCAGGGTAATTAAGT
78615 CTGGTAAGAA
Statistics
Matches: 162, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
141 40 0.25
142 122 0.75
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (141 bp):
AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTCGGTAATCAACTTAATTCAGGGTAATTAAGT
GAGTCAGTAATCAACTTTAATTCAGGGTAACTAAGTGAGTTAATAAGTAACTTAATTCAGGGTAA
TTAAGTAGTTC
Found at i:87404 original size:14 final size:14
Alignment explanation
Indices: 87385--87411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87375 TCCCATCTTA
87385 ATCAGTTTGCATTG
1 ATCAGTTTGCATTG
87399 ATCAGTTTGCATT
1 ATCAGTTTGCATT
87412 CATGGCGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (14 bp):
ATCAGTTTGCATTG
Found at i:88050 original size:13 final size:12
Alignment explanation
Indices: 88022--88049 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
88012 CAAAGTTTGG
88022 TTTTCTTGTTTT
1 TTTTCTTGTTTT
88034 TTTTCTTGTTTT
1 TTTTCTTGTTTT
88046 TTTT
1 TTTT
88050 TTGGAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTCTTGTTTT
Found at i:91172 original size:21 final size:21
Alignment explanation
Indices: 91148--91188 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
91138 TATCGCTGGC
91148 CTGTACAGTATCTAATCTCAT
1 CTGTACAGTATCTAATCTCAT
* *
91169 CTGTACAGTGTTTAATCTCA
1 CTGTACAGTATCTAATCTCA
91189 CCATTTCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (21 bp):
CTGTACAGTATCTAATCTCAT
Found at i:92938 original size:30 final size:28
Alignment explanation
Indices: 92902--92993 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 28
92892 TCAGAAAAGA
92902 GCTTATTTGGCCTTTTTAAAGAGTTCAGGG
1 GCTTATTTGGCCTTTTT-AA-AGTTCAGGG
**
92932 GCTTATTTGG-CTGCAATTAAAGTTCAGGG
1 GCTTATTTGGCCT--TTTTAAAGTTCAGGG
*
92961 GCTTATTTGGCCGTTTTGTGTAAGTTCAGGG
1 GCTTATTTGGCC-TTTT-T-AAAGTTCAGGG
92992 GC
1 GC
92994 CTTTTTGAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
29 22 0.43
30 14 0.27
31 15 0.29
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.38
Consensus pattern (28 bp):
GCTTATTTGGCCTTTTTAAAGTTCAGGG
Found at i:94680 original size:2 final size:2
Alignment explanation
Indices: 94673--94702 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
94663 GAATATTCAA
94673 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
94703 ACTTGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:104835 original size:9 final size:9
Alignment explanation
Indices: 104821--104870 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
104811 CGAACCCGAT
104821 AACCCGCCC
1 AACCCGCCC
104830 AACCCGCCC
1 AACCCGCCC
* *
104839 GAATCCG--T
1 -AACCCGCCC
104847 AACCCGCCC
1 AACCCGCCC
104856 AACCCGCCC
1 AACCCGCCC
104865 AACCCG
1 AACCCG
104871 ATTTGACCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 5 0.15
9 24 0.71
10 5 0.15
ACGTcount: A:0.24, C:0.58, G:0.14, T:0.04
Consensus pattern (9 bp):
AACCCGCCC
Found at i:104851 original size:26 final size:27
Alignment explanation
Indices: 104809--104872 Score: 105
Period size: 26 Copynumber: 2.4 Consensus size: 27
104799 CAAAATCTGA
104809 CCCGAACCCGATAACCCGCCCAACCCG
1 CCCGAACCCGATAACCCGCCCAACCCG
*
104836 CCCGAATCCG-TAACCCGCCCAACCCG
1 CCCGAACCCGATAACCCGCCCAACCCG
104862 CCC-AACCCGAT
1 CCCGAACCCGAT
104873 TTGACCAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 5 0.15
26 20 0.59
27 9 0.26
ACGTcount: A:0.25, C:0.55, G:0.14, T:0.06
Consensus pattern (27 bp):
CCCGAACCCGATAACCCGCCCAACCCG
Found at i:104928 original size:16 final size:16
Alignment explanation
Indices: 104916--105026 Score: 136
Period size: 16 Copynumber: 6.9 Consensus size: 16
104906 CGAACCCGTG
*
104916 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGAA
*
104932 ACCC-AGATGACCCGAG
1 ACCCGA-ATGACCCGAA
*
104948 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGAA
104964 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGAA
*
104980 ACCCGAATGACCCGAG
1 ACCCGAATGACCCGAA
*
104996 ACCCGTATGACCCGAA
1 ACCCGAATGACCCGAA
*
105012 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
105027 GACATTAACC
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
15 2 0.02
16 77 0.95
17 2 0.02
ACGTcount: A:0.33, C:0.38, G:0.20, T:0.09
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:104961 original size:48 final size:47
Alignment explanation
Indices: 104896--105026 Score: 158
Period size: 48 Copynumber: 2.7 Consensus size: 47
104886 GTAAACGACT
* * *
104896 CGAGACCCGACGAACCCGTGACCCGAATGACCCGTAACCC-AGATGACC
1 CGAGACCCGATG-ACCCGTAACCCGAATGACCCGAAACCCGA-ATGACC
104944 CGAGACCCGAATGACCCGTAACCC-AGATGACCCGAAACCCGAATGACC
1 CGAGACCCG-ATGACCCGTAACCCGA-ATGACCCGAAACCCGAATGACC
* *
104992 CGAGACCCGTATGACCCGAAACCCGAATAACCCGA
1 CGAGACCCG-ATGACCCGTAACCCGAATGACCCGA
105027 GACATTAACC
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
47 1 0.01
48 68 0.93
49 4 0.05
ACGTcount: A:0.32, C:0.38, G:0.21, T:0.08
Consensus pattern (47 bp):
CGAGACCCGATGACCCGTAACCCGAATGACCCGAAACCCGAATGACC
Found at i:105029 original size:32 final size:32
Alignment explanation
Indices: 104916--105025 Score: 170
Period size: 32 Copynumber: 3.4 Consensus size: 32
104906 CGAACCCGTG
*
104916 ACCCGAATGACCCGTAACCCAGATGACCCGAG
1 ACCCGAATGACCCGTAACCCAGATGACCCGAA
104948 ACCCGAATGACCCGTAACCCAGATGACCCGAA
1 ACCCGAATGACCCGTAACCCAGATGACCCGAA
104980 ACCCGAATGACCCG-AGACCC-GTATGACCCGAA
1 ACCCGAATGACCCGTA-ACCCAG-ATGACCCGAA
*
105012 ACCCGAATAACCCG
1 ACCCGAATGACCCG
105026 AGACATTAAC
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
31 2 0.03
32 72 0.97
ACGTcount: A:0.33, C:0.38, G:0.20, T:0.09
Consensus pattern (32 bp):
ACCCGAATGACCCGTAACCCAGATGACCCGAA
Found at i:105160 original size:21 final size:21
Alignment explanation
Indices: 105135--105181 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
105125 TACAATTTAT
*
105135 ATTATTGTTATAATTTTACCA
1 ATTATTATTATAATTTTACCA
* *
105156 ATTATTATTATGATTTTACCT
1 ATTATTATTATAATTTTACCA
105177 ATTAT
1 ATTAT
105182 AAATTGGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTATTATTATAATTTTACCA
Found at i:105664 original size:16 final size:16
Alignment explanation
Indices: 105630--105762 Score: 157
Period size: 16 Copynumber: 8.4 Consensus size: 16
105620 AACCCGCCCA
105630 ACCCGAGACCCG-ATAG
1 ACCCGAGACCCGAAT-G
* *
105646 ACCTGAGGCCCGAATG
1 ACCCGAGACCCGAATG
*
105662 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
*
105678 ACCCGAGGCCCGAATG
1 ACCCGAGACCCGAATG
105694 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* *
105710 ACCCGATACCCGAATA
1 ACCCGAGACCCGAATG
105726 ACCCGA-ACCC-AGATG
1 ACCCGAGACCCGA-ATG
105741 ACCCGTA-ACCCGAATG
1 ACCCG-AGACCCGAATG
105757 ACCCGA
1 ACCCGA
105763 AAAAACTACA
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
14 1 0.01
15 12 0.12
16 86 0.84
17 3 0.03
ACGTcount: A:0.32, C:0.38, G:0.23, T:0.08
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:105666 original size:9 final size:9
Alignment explanation
Indices: 105654--105763 Score: 86
Period size: 9 Copynumber: 13.7 Consensus size: 9
105644 AGACCTGAGG
105654 CCCGAATGA
1 CCCGAATGA
105663 CCCGAA--A
1 CCCGAATGA
105670 CCCGAATGA
1 CCCGAATGA
*
105679 CCCG-A-GG
1 CCCGAATGA
105686 CCCGAATGA
1 CCCGAATGA
105695 CCCG-A-GA
1 CCCGAATGA
105702 CCCGAATGA
1 CCCGAATGA
105711 CCCG-AT-A
1 CCCGAATGA
*
105718 CCCGAATAA
1 CCCGAATGA
105727 CCCG-A--A
1 CCCGAATGA
105733 CCC-AGATGA
1 CCCGA-ATGA
*
105742 CCCG--TAA
1 CCCGAATGA
105749 CCCGAATGA
1 CCCGAATGA
105758 CCCGAA
1 CCCGAA
105764 AAAACTACAT
Statistics
Matches: 82, Mismatches: 4, Indels: 30
0.71 0.03 0.26
Matches are distributed among these distances:
6 4 0.05
7 30 0.37
8 9 0.11
9 39 0.48
ACGTcount: A:0.33, C:0.38, G:0.21, T:0.08
Consensus pattern (9 bp):
CCCGAATGA
Found at i:106714 original size:25 final size:25
Alignment explanation
Indices: 106680--106730 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
106670 AATTAAAACG
106680 TTTCTGAAAATAAGAGGTGGCAATT
1 TTTCTGAAAATAAGAGGTGGCAATT
106705 TTTCTGAAAATAAGAGGTGGCAATT
1 TTTCTGAAAATAAGAGGTGGCAATT
106730 T
1 T
106731 GCTAGATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (25 bp):
TTTCTGAAAATAAGAGGTGGCAATT
Found at i:112336 original size:16 final size:16
Alignment explanation
Indices: 112318--112392 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
112308 ATTTTTGGGT
*
112318 ACCCAAACCCGAAATT
1 ACCCAAACCCGAAATG
* * *
112334 ACCCGAATCC-AAACG
1 ACCCAAACCCGAAATG
112349 ACCCAAACCCGAAATG
1 ACCCAAACCCGAAATG
*
112365 ACCCAAACCCAAAATG
1 ACCCAAACCCGAAATG
*
112381 ACCCGAACCCGA
1 ACCCAAACCCGA
112393 TCAACCCGAC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 11 0.23
16 37 0.77
ACGTcount: A:0.43, C:0.40, G:0.11, T:0.07
Consensus pattern (16 bp):
ACCCAAACCCGAAATG
Found at i:112356 original size:31 final size:32
Alignment explanation
Indices: 112318--112392 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
112308 ATTTTTGGGT
* * *
112318 ACCCAAACCCGAAATTACCCGAATCC-AAACG
1 ACCCAAACCCGAAATGACCCAAACCCAAAACG
*
112349 ACCCAAACCCGAAATGACCCAAACCCAAAATG
1 ACCCAAACCCGAAATGACCCAAACCCAAAACG
*
112381 ACCCGAACCCGA
1 ACCCAAACCCGA
112393 TCAACCCGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 23 0.61
32 15 0.39
ACGTcount: A:0.43, C:0.40, G:0.11, T:0.07
Consensus pattern (32 bp):
ACCCAAACCCGAAATGACCCAAACCCAAAACG
Found at i:113433 original size:11 final size:11
Alignment explanation
Indices: 113414--113444 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
113404 GAAAGTCTAT
*
113414 TATATTATATA
1 TATAGTATATA
113425 TATAGTATATA
1 TATAGTATATA
113436 TATAGTATA
1 TATAGTATA
113445 AATCAGAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (11 bp):
TATAGTATATA
Found at i:113748 original size:16 final size:16
Alignment explanation
Indices: 113727--113757 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
113717 AATTGTAACA
113727 AACCGAACCCGAAAAG
1 AACCGAACCCGAAAAG
113743 AACCGAACCCGAAAA
1 AACCGAACCCGAAAA
113758 CCCGAGGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (16 bp):
AACCGAACCCGAAAAG
Done.