Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 29
Found at i:6057428 original size:18 final size:18
Alignment explanation
Indices: 6057405--6057455 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 18
6057395 AATACTAAGA
6057405 GGTATCGATACCCCTATG
1 GGTATCGATACCCCTATG
*
6057423 GGTATCCATACCCC---G
1 GGTATCGATACCCCTATG
6057438 GGTATCGATACCCCTATG
1 GGTATCGATACCCCTATG
6057456 AATGGGTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 14 0.50
18 14 0.50
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (18 bp):
GGTATCGATACCCCTATG
Found at i:6057465 original size:22 final size:22
Alignment explanation
Indices: 6057437--6057479 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6057427 TCCATACCCC
*
6057437 GGGTATCGATACCCCTATGAAT
1 GGGTATCAATACCCCTATGAAT
6057459 GGGTATCAATACCCCTATGAA
1 GGGTATCAATACCCCTATGAA
6057480 GACTCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (22 bp):
GGGTATCAATACCCCTATGAAT
Found at i:6057471 original size:37 final size:33
Alignment explanation
Indices: 6057405--6057473 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 33
6057395 AATACTAAGA
*
6057405 GGTATCGATACCCCTATGGGTATCCATACCCCG
1 GGTATCGATACCCCTATGGGTATCAATACCCCG
6057438 GGTATCGATACCCCTATGAATGGGTATCAATACCCC
1 GGTATCGATACCCC--T--ATGGGTATCAATACCCC
6057474 TATGAAGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 14 0.45
35 1 0.03
37 16 0.52
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (33 bp):
GGTATCGATACCCCTATGGGTATCAATACCCCG
Found at i:6057953 original size:34 final size:33
Alignment explanation
Indices: 6057914--6057984 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
6057904 CTTTGTAAAG
*
6057914 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAAGCCCGTG-AAAAACTA
* * *
6057948 GGGAAATGTTCTAGTTTAGCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
6057981 GGGA
1 GGGA
6057985 GTTTGTAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:6064692 original size:21 final size:21
Alignment explanation
Indices: 6064666--6064706 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6064656 ATTCTAAAGT
*
6064666 ATCAGGAAATTGTTCAGATAC
1 ATCAGGAAAGTGTTCAGATAC
6064687 ATCAGGAAAGTGTTCAGATA
1 ATCAGGAAAGTGTTCAGATA
6064707 TGACTGGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (21 bp):
ATCAGGAAAGTGTTCAGATAC
Found at i:6065834 original size:8 final size:8
Alignment explanation
Indices: 6065814--6065874 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
6065804 ATTTTTAAGA
6065814 ATTTTAA-
1 ATTTTAAT
6065821 ATTTTAAT
1 ATTTTAAT
6065829 ATTTT-AT
1 ATTTTAAT
*
6065836 AATTCTAAT
1 -ATTTTAAT
6065845 ATTTT--T
1 ATTTTAAT
6065851 ATTTTAAAT
1 ATTTT-AAT
*
6065860 ATTTTTAT
1 ATTTTAAT
6065868 ATTTTAA
1 ATTTTAA
6065875 AATTCTTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
6 6 0.14
7 9 0.20
8 21 0.48
9 8 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTAAT
Found at i:6065839 original size:16 final size:16
Alignment explanation
Indices: 6065791--6065874 Score: 68
Period size: 16 Copynumber: 5.2 Consensus size: 16
6065781 TTAAACATTC
*
6065791 TAATACTTTATACATTTT
1 TAATATTTTATA-A-TTT
*
6065809 TAAGAATTTTA-AATTT
1 TAA-TATTTTATAATTT
*
6065825 TAATATTTTATAATTC
1 TAATATTTTATAATTT
6065841 TAATATTTT-T-ATTT
1 TAATATTTTATAATTT
6065855 TAAATATTTT-TATATTT
1 T-AATATTTTATA-ATTT
6065872 TAA
1 TAA
6065875 AATTCTTTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 4 0.07
15 16 0.29
16 21 0.38
17 6 0.11
18 4 0.07
19 5 0.09
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (16 bp):
TAATATTTTATAATTT
Found at i:6066686 original size:36 final size:36
Alignment explanation
Indices: 6066589--6067055 Score: 463
Period size: 36 Copynumber: 13.0 Consensus size: 36
6066579 CAAGTCTCCG
* *
6066589 CCTCCTCCCCCCAAGGAGTCATACAAGTATAAGTCT
1 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
* * **** *
6066625 CCACCTCCACCTCCTCCAGT-TTACAAGTACAAGTCT
1 CCTCCTCCTCC-CAAGGAGTCATACAAGTACAAGTCT
*
6066661 CCTCCTCCTCCTAAGGAGTCATACAAGTACAAGTCT
1 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
6066697 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
1 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
6066733 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
1 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
6066769 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
1 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
* * *
6066805 CCTCCTCC-ACC------TCCT-CCAGTCTACAAGTCT
1 CCTCCTCCTCCCAAGGAGTCATACAAG--TACAAGTCT
* * *
6066835 CCTCCTCCTCCCAAGGAGACATACAAGTATAAGTCA
1 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
* * * * **
6066871 CCACCGCCACCCCCACCAGTC-TACAAGTACAAGTCT
1 CCTCCTCC-TCCCAAGGAGTCATACAAGTACAAGTCT
*
6066907 CCTCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCT
1 CCTCCTCCT-C-CC-AAGGAGTCATACAAGTACAAGTCT
*
6066946 CCTCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCT
1 CCTCCTCCT-C-CC-AAGGAGTCATACAAGTACAAGTCT
* * *** *
6066985 CCACCTCCACCTCCTCCG-GT-TTACAAGTACAAGTCT
1 CCTCCTCC-TC-CCAAGGAGTCATACAAGTACAAGTCT
*
6067021 CCTCCTCCTCCCAAGGAGACATACAAGTACAAGTC
1 CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTC
6067056 ACCACCACCA
Statistics
Matches: 355, Mismatches: 56, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.01
29 3 0.01
30 17 0.05
31 2 0.01
34 3 0.01
35 7 0.02
36 231 0.65
37 16 0.05
38 8 0.02
39 65 0.18
ACGTcount: A:0.27, C:0.39, G:0.12, T:0.22
Consensus pattern (36 bp):
CCTCCTCCTCCCAAGGAGTCATACAAGTACAAGTCT
Found at i:6067067 original size:72 final size:75
Alignment explanation
Indices: 6066931--6067072 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 75
6066921 TAAGGAGCCA
* * *
6066931 TACAAGTACAAGTCTCCTCCTCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCACCTCCACC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCTAAGGAGACATACAAGTACAAGTCACCACCACCACC
6066996 TCCTCCGGTT
66 TCCTCCGGTT
6067006 TACAAGTACAAGTCTCCTCCTCCT-C-CC-AAGGAGACATACAAGTACAAGTCACCACCACCACC
1 TACAAGTACAAGTCTCCTCCTCCTCCTCCTAAGGAGACATACAAGTACAAGTCACCACCACCACC
6067068 TCCTC
66 TCCTC
6067073 ACCACTACTA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
72 37 0.58
73 2 0.03
74 1 0.02
75 24 0.38
ACGTcount: A:0.27, C:0.40, G:0.11, T:0.21
Consensus pattern (75 bp):
TACAAGTACAAGTCTCCTCCTCCTCCTCCTAAGGAGACATACAAGTACAAGTCACCACCACCACC
TCCTCCGGTT
Found at i:6071367 original size:32 final size:32
Alignment explanation
Indices: 6071321--6071402 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
6071311 ATACTAGCAG
* *
6071321 TGTTGCATTCAGATAATGAACATCAGAGTCAA
1 TGTTGCATTTAGATAATGAACAGCAGAGTCAA
* * * *
6071353 TGTTGCATTTAGATAATGCACAGGAGTGTCAG
1 TGTTGCATTTAGATAATGAACAGCAGAGTCAA
**
6071385 TGTCACATTTAGATAATG
1 TGTTGCATTTAGATAATG
6071403 CATAGCAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (32 bp):
TGTTGCATTTAGATAATGAACAGCAGAGTCAA
Found at i:6073638 original size:19 final size:19
Alignment explanation
Indices: 6073610--6073646 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6073600 ATTTCTGTAT
6073610 ATCATATAATACATATAAC
1 ATCATATAATACATATAAC
* *
6073629 ATCATGTAATTCATATAA
1 ATCATATAATACATATAA
6073647 TACATTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (19 bp):
ATCATATAATACATATAAC
Found at i:6073991 original size:20 final size:23
Alignment explanation
Indices: 6073952--6073993 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
6073942 GTACTCATGT
6073952 CATTTCTCTTGTGATCACATATG
1 CATTTCTCTTGTGATCACATATG
6073975 CATTTCT-TT-TG-TCACATAT
1 CATTTCTCTTGTGATCACATAT
6073994 CACATGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 2 0.11
23 7 0.37
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (23 bp):
CATTTCTCTTGTGATCACATATG
Found at i:6089191 original size:13 final size:14
Alignment explanation
Indices: 6089180--6089212 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
6089170 TTGTTTTTTG
6089180 AAAATATTTTTTAA
1 AAAATATTTTTTAA
6089194 AAAATA-TTTTTAA
1 AAAATATTTTTTAA
6089207 AAAATA
1 AAAATA
6089213 AATTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATATTTTTTAA
Found at i:6089335 original size:19 final size:19
Alignment explanation
Indices: 6089311--6089347 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6089301 ATTTATTACA
6089311 AATATTAAATATAATAAAT
1 AATATTAAATATAATAAAT
**
6089330 AATATTATTTATAATAAA
1 AATATTAAATATAATAAA
6089348 ACTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATTAAATATAATAAAT
Found at i:6089548 original size:23 final size:23
Alignment explanation
Indices: 6089499--6089549 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
6089489 GTGTTATACT
**
6089499 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
6089522 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
6089545 ATATT
1 ATATT
6089550 ATTTGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:6089605 original size:19 final size:19
Alignment explanation
Indices: 6089537--6089617 Score: 55
Period size: 19 Copynumber: 4.3 Consensus size: 19
6089527 TTAAATATCT
*
6089537 TTATTAA-AATATTATTTGA
1 TTATTAATAATATTA-TTAA
6089556 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
6089575 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
6089595 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
6089613 -TATTA
1 TTATTA
6089618 TTTCTATGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.26
19 18 0.36
20 7 0.14
22 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:6089716 original size:23 final size:23
Alignment explanation
Indices: 6089682--6089732 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
6089672 TTAAAATAAA
*
6089682 AATATAATTGATTATATTATTAT
1 AATATAACTGATTATATTATTAT
*
6089705 AATATAACTGATTATTTTATTAT
1 AATATAACTGATTATATTATTAT
6089728 AATAT
1 AATAT
6089733 TAAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
AATATAACTGATTATATTATTAT
Found at i:6089747 original size:22 final size:22
Alignment explanation
Indices: 6089717--6089765 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
6089707 TATAACTGAT
*
6089717 TATTTTATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
6089739 TATTATATTATATTATTATAAA
1 TATTATATTATAATATTAAAAA
6089761 TATTA
1 TATTA
6089766 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:6089755 original size:30 final size:32
Alignment explanation
Indices: 6089715--6089773 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
6089705 AATATAACTG
*
6089715 ATTATTTTATTAT-AATATTAA-AAATATTAT
1 ATTATATTATTATAAATATTAATAAATATTAT
6089745 ATTATATTATTATAAATATTAATAAATAT
1 ATTATATTATTATAAATATTAATAAATAT
6089774 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 12 0.46
31 8 0.31
32 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTATATTATTATAAATATTAATAAATATTAT
Found at i:6089773 original size:22 final size:21
Alignment explanation
Indices: 6089729--6089785 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
6089719 TTTTATTATA
* *
6089729 ATATTAAAAATATTATATTAT
1 ATATTATAAATATTATATAAT
6089750 ATTATTATAAATATTA-ATAAAT
1 A-TATTATAAATATTATAT-AAT
*
6089772 ATATTTTAAATATT
1 ATATTATAAATATT
6089786 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTATAAATATTATATAAT
Found at i:6094715 original size:20 final size:20
Alignment explanation
Indices: 6094690--6094738 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
6094680 ACACCACCAT
6094690 ATGCAACTATATAGACCTAA
1 ATGCAACTATATAGACCTAA
*
6094710 ATGCAACTATATAGGCCTAA
1 ATGCAACTATATAGACCTAA
6094730 ATGCAACTA
1 ATGCAACTA
6094739 AATGCAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (20 bp):
ATGCAACTATATAGACCTAA
Found at i:6095305 original size:26 final size:26
Alignment explanation
Indices: 6095275--6095332 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
6095265 ATATTATAGT
6095275 TGTCATTTATTCAAGGGGGTTTCCAA
1 TGTCATTTATTCAAGGGGGTTTCCAA
6095301 TGTCATTTATTCAAGGGGGTTTCCAA
1 TGTCATTTATTCAAGGGGGTTTCCAA
6095327 TGTCAT
1 TGTCAT
6095333 AGCAAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (26 bp):
TGTCATTTATTCAAGGGGGTTTCCAA
Found at i:6097567 original size:109 final size:110
Alignment explanation
Indices: 6097408--6097608 Score: 271
Period size: 109 Copynumber: 1.8 Consensus size: 110
6097398 AATAAGGGGG
* * * *
6097408 CTAAATAGAAAATATTCCAATAAACACATAACATACAAGAAAAAAGGGTAAATAATAATTTTGGT
1 CTAAATAGAAAATATCCCAAAAAACACATAACATACAAGAAAAAAGGGTAAATAACAACTTTGGT
6097473 CCCTA-AAGGTGACCAACATGCAAAAATGTCATAAACTATGGGAGA
66 CCCTACAA-GTGACCAACATGCAAAAATGTCATAAACTATGGGAGA
* * * ** *
6097518 CTAAATAGAAAATATCCCAAAAAATATATAACGTGTAAG-GAAAAGGGTAAATAACAACTTTGGT
1 CTAAATAGAAAATATCCCAAAAAACACATAACATACAAGAAAAAAGGGTAAATAACAACTTTGGT
* *
6097582 CCTTACAAGTGACCAGCATGCAAAAAT
66 CCCTACAAGTGACCAACATGCAAAAAT
6097609 ACTCTAGACT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
109 44 0.56
110 34 0.44
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (110 bp):
CTAAATAGAAAATATCCCAAAAAACACATAACATACAAGAAAAAAGGGTAAATAACAACTTTGGT
CCCTACAAGTGACCAACATGCAAAAATGTCATAAACTATGGGAGA
Found at i:6099300 original size:23 final size:23
Alignment explanation
Indices: 6099273--6099326 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
6099263 GTTGGTTCTA
*
6099273 TCAATCTCAAAAGTCATTTACAT
1 TCAATCACAAAAGTCATTTACAT
6099296 TCAATCACAAAAGTCATTTACAT
1 TCAATCACAAAAGTCATTTACAT
6099319 TCAATCAC
1 TCAATCAC
6099327 TGCCATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (23 bp):
TCAATCACAAAAGTCATTTACAT
Found at i:6104154 original size:2 final size:2
Alignment explanation
Indices: 6104090--6104141 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
6104080 AGATATGATA
6104090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6104132 AT AT AT AT AT
1 AT AT AT AT AT
6104142 CAAAGTCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6105082 original size:31 final size:29
Alignment explanation
Indices: 6105040--6105208 Score: 96
Period size: 31 Copynumber: 5.6 Consensus size: 29
6105030 TATAACAAAT
*
6105040 AAGTACTTAAAAGTATATCATTTTTTCATCA
1 AAGTACCT-AAAGTAT-TCATTTTTTCATCA
* * **
6105071 AAGTACCTAAAATATT--TTTTAGTCAAAA
1 AAGTACCTAAAGTATTCATTTT-TTCATCA
*
6105099 TAAGTACCTAAAGT-TATC-TTTTTGGTCA-AA
1 -AAGTACCTAAAGTAT-TCATTTTT--TCATCA
* *
6105129 ATATTACCTAAAGTATTCAATTTTTTTCATCT
1 A-AGTACCTAAAGTATTC-A-TTTTTTCATCA
* * *
6105161 AAGTAACTAAAATATTCAATTTTTTTCATCT
1 AAGTACCTAAAGTATTC-A-TTTTTTCATCA
6105192 AAGTACCTAAAGTATTC
1 AAGTACCTAAAGTATTC
6105209 TTTAATTAAT
Statistics
Matches: 111, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
27 4 0.04
28 5 0.05
29 15 0.14
30 25 0.23
31 56 0.50
32 1 0.01
33 5 0.05
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (29 bp):
AAGTACCTAAAGTATTCATTTTTTCATCA
Found at i:6105107 original size:29 final size:29
Alignment explanation
Indices: 6105071--6105145 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
6105061 TTTTTCATCA
6105071 AAGTACCTAAAATATTTTTTAGTCAAAAT
1 AAGTACCTAAAATATTTTTTAGTCAAAAT
* *
6105100 AAGTACCTAAAGTTATCTTTTTGGTCAAAAT
1 AAGTACCTAAA-ATAT-TTTTTAGTCAAAAT
* *
6105131 -ATTACCTAAAGTATT
1 AAGTACCTAAAATATT
6105146 CAATTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 14 0.35
30 12 0.30
31 13 0.32
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (29 bp):
AAGTACCTAAAATATTTTTTAGTCAAAAT
Found at i:6105139 original size:30 final size:30
Alignment explanation
Indices: 6105071--6105142 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
6105061 TTTTTCATCA
*
6105071 AAGTACCTAAA-ATATTTTTTAGTCAAAAT
1 AAGTACCTAAAGTTATTTTTTAGTCAAAAT
*
6105100 AAGTACCTAAAGTTATCTTTTTGGTCAAAAT
1 AAGTACCTAAAGTTAT-TTTTTAGTCAAAAT
*
6105131 -ATTACCTAAAGT
1 AAGTACCTAAAGT
6105143 ATTCAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.29
30 14 0.37
31 13 0.34
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (30 bp):
AAGTACCTAAAGTTATTTTTTAGTCAAAAT
Found at i:6105298 original size:29 final size:29
Alignment explanation
Indices: 6105261--6105319 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
6105251 AAAAAGATTG
*
6105261 AATATTTTAAGTACCTATTTTGACAAAAA
1 AATACTTTAAGTACCTATTTTGACAAAAA
* * *
6105290 AATACTTTAGGTACCTATTTTTACCAAAA
1 AATACTTTAAGTACCTATTTTGACAAAAA
6105319 A
1 A
6105320 GATAAGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (29 bp):
AATACTTTAAGTACCTATTTTGACAAAAA
Found at i:6105363 original size:29 final size:30
Alignment explanation
Indices: 6105284--6105366 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 30
6105274 CCTATTTTGA
* * * * *
6105284 CAAAAAAATACTTTAGGTACCTATTTTTAC
1 CAAAAAGATAGTTTAGGTACTTATGTTAAC
*
6105314 CAAAAAGATAAGTTTACGTACTTATGTTAAC
1 CAAAAAGAT-AGTTTAGGTACTTATGTTAAC
6105345 C-AAAAGATAGTTTAGGTACTTA
1 CAAAAAGATAGTTTAGGTACTTA
6105367 AATGAAAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.29
30 15 0.33
31 17 0.38
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (30 bp):
CAAAAAGATAGTTTAGGTACTTATGTTAAC
Found at i:6110296 original size:71 final size:71
Alignment explanation
Indices: 6110169--6110307 Score: 197
Period size: 71 Copynumber: 2.0 Consensus size: 71
6110159 CATTCCAAAA
* * * * * *
6110169 AAAAAGGATCGATCCCTCGACCAAAAAGATCGATCCCAAACTTTTTGTTGTTTAAAGGATCGATC
1 AAAAAGAATCGATCCCTCAACCAAAAAGATCGATCCCAAACATTTTATTGTGTAAAGGATCGACC
6110234 CCTGGG
66 CCTGGG
* * *
6110240 AAAAAGAATCGATCCCTCAACCAAAAGGATTGATCTCAAACATTTTATTGTGTAAAGGATCGACC
1 AAAAAGAATCGATCCCTCAACCAAAAAGATCGATCCCAAACATTTTATTGTGTAAAGGATCGACC
6110305 CCT
66 CCT
6110308 TTTCAAAAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (71 bp):
AAAAAGAATCGATCCCTCAACCAAAAAGATCGATCCCAAACATTTTATTGTGTAAAGGATCGACC
CCTGGG
Found at i:6112980 original size:37 final size:37
Alignment explanation
Indices: 6112938--6113013 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
6112928 GGGCAATCGT
6112938 AATTCAAAAAATTGATACAGGGAGCAG-ATGCAATTGC
1 AATTCAAAAAATTGATACAGGGAGCAGAAT-CAATTGC
* * *
6112975 AATTCAGAAAATTGATAGATGGAGCAGAATCAATTGC
1 AATTCAAAAAATTGATACAGGGAGCAGAATCAATTGC
6113012 AA
1 AA
6113014 AGAAGATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 33 0.94
38 2 0.06
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (37 bp):
AATTCAAAAAATTGATACAGGGAGCAGAATCAATTGC
Found at i:6113033 original size:34 final size:35
Alignment explanation
Indices: 6112945--6113034 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 35
6112935 CGTAATTCAA
* *
6112945 AAAATTGATACAGGGAGCAGATGCAATTGCAATTCAG
1 AAAATTAATAGAGGGAGCAGATGCAATTGCAA-T-AG
* *
6112982 AAAATTGATAGATGGAGCAGAAT-CAATTGCAA-AG
1 AAAATTAATAGAGGGAGCAG-ATGCAATTGCAATAG
*
6113016 AAGATTAATAGAGGGAGCA
1 AAAATTAATAGAGGGAGCA
6113035 TTTCAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 18 0.38
37 27 0.57
38 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.20
Consensus pattern (35 bp):
AAAATTAATAGAGGGAGCAGATGCAATTGCAATAG
Found at i:6116110 original size:34 final size:34
Alignment explanation
Indices: 6116042--6116256 Score: 267
Period size: 34 Copynumber: 6.7 Consensus size: 34
6116032 AAATTTTTAA
6116042 AATAATTAACTTGATTTTATAATAA-TTATGCAT
1 AATAATTAACTTGATTTTATAATAATTTATGCAT
6116075 AATAATTAACTTGATTTTATAATAATTTATGCAT
1 AATAATTAACTTGATTTTATAATAATTTATGCAT
6116109 AATAATTAACTTGATTTTATAATAATTTATGCAT
1 AATAATTAACTTGATTTTATAATAATTTATGCAT
*
6116143 AATAATTAACTTTATTTT-TAATAATTTATG--T
1 AATAATTAACTTGATTTTATAATAATTTATGCAT
* *
6116174 -AT-A-T-ATTTGATTTTATAATAA-TTA-AC-T
1 AATAATTAACTTGATTTTATAATAATTTATGCAT
* *
6116201 --TAATTAACTTGATTTTGTAATAATTTATGCAA
1 AATAATTAACTTGATTTTATAATAATTTATGCAT
* * *
6116233 AAGAATTAACTTTATTTTGTAATA
1 AATAATTAACTTGATTTTATAATA
6116257 TTTTTATCTT
Statistics
Matches: 161, Mismatches: 10, Indels: 21
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.01
27 13 0.08
28 8 0.05
29 16 0.10
30 5 0.03
31 2 0.01
33 37 0.23
34 79 0.49
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.48
Consensus pattern (34 bp):
AATAATTAACTTGATTTTATAATAATTTATGCAT
Found at i:6117320 original size:16 final size:16
Alignment explanation
Indices: 6117296--6117326 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6117286 GCAAAGTTAT
*
6117296 AAAATTATAAATAAAG
1 AAAAATATAAATAAAG
6117312 AAAAATATAAATAAA
1 AAAAATATAAATAAA
6117327 TAATTGAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAATATAAATAAAG
Found at i:6117358 original size:19 final size:18
Alignment explanation
Indices: 6117314--6117361 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
6117304 AAATAAAGAA
6117314 AAATATAAATAAATAATTG
1 AAAT-TAAATAAATAATTG
* *
6117333 AAGTTAAATAAATTAATTT
1 AAATTAAATAAA-TAATTG
6117352 AAATTAAATA
1 AAATTAAATA
6117362 CTATAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAATTAAATAAATAATTG
Found at i:6117377 original size:5 final size:5
Alignment explanation
Indices: 6117369--6117413 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
6117359 ATACTATAAT
6117369 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
6117414 CATATTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:6118433 original size:21 final size:20
Alignment explanation
Indices: 6118399--6118442 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6118389 TTAATATTTT
*
6118399 TAATATTTAATAAACAATTA
1 TAATATTTAATAAACAATAA
* *
6118419 TAATATTTTATTAAATAATAA
1 TAATA-TTTAATAAACAATAA
6118440 TAA
1 TAA
6118443 CACCATTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATATTTAATAAACAATAA
Found at i:6118756 original size:17 final size:18
Alignment explanation
Indices: 6118724--6118762 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6118714 GAATTCAATT
*
6118724 TAAAGATTACATTTAATA
1 TAAACATTACATTTAATA
*
6118742 TAAACATTA-ATTTAATC
1 TAAACATTACATTTAATA
6118759 TAAA
1 TAAA
6118763 AATAATCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAACATTACATTTAATA
Found at i:6119117 original size:20 final size:20
Alignment explanation
Indices: 6119080--6119144 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
6119070 CACGAACCGA
*
6119080 TTCTCTTCT-TCTTATTTCT
1 TTCTCTTTTCTCTTATTTCT
*
6119099 TTCTCTTTTCTCTTCTTTCT
1 TTCTCTTTTCTCTTATTTCT
* *
6119119 TCCTCTTTTCTCTTTTTTC-
1 TTCTCTTTTCTCTTATTTCT
6119138 TTCTCTT
1 TTCTCTT
6119145 CTTTCTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCTCTTTTCTCTTATTTCT
Found at i:6119143 original size:12 final size:12
Alignment explanation
Indices: 6119086--6119151 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
6119076 CCGATTCTCT
6119086 TCTTCTTAT-TTC
1 TCTTCTT-TCTTC
6119098 T-TTCTCTT-TTC
1 TCTTCT-TTCTTC
6119109 TCTTCTTTCTTC
1 TCTTCTTTCTTC
6119121 -C-TC-TT-TTC
1 TCTTCTTTCTTC
*
6119129 TCTTTTTTCTTC
1 TCTTCTTTCTTC
6119141 TCTTCTTTCTT
1 TCTTCTTTCTT
6119152 TCACTCCCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 3 0.07
11 14 0.31
12 22 0.49
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTCTTTCTTC
Found at i:6119193 original size:2 final size:2
Alignment explanation
Indices: 6119186--6119216 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6119176 CCTACACCTC
6119186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6119217 ACCCAACCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6120763 original size:23 final size:23
Alignment explanation
Indices: 6120735--6120781 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
6120725 TTGCTTAAGG
*
6120735 GAAATGGTGATTGAGAAACTTTT
1 GAAATGGTGATTGAAAAACTTTT
*
6120758 GAAATGGTGGTTGAAAAACTTTT
1 GAAATGGTGATTGAAAAACTTTT
6120781 G
1 G
6120782 GACATGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (23 bp):
GAAATGGTGATTGAAAAACTTTT
Found at i:6121235 original size:42 final size:42
Alignment explanation
Indices: 6121189--6121273 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
6121179 TTAATCGAAT
*
6121189 TCGTCAATAATTTATCAAAAATAATTCAAAGTTCAAATTAAC
1 TCGTCAATAATTTATCAAAAATAATTCAAAGTCCAAATTAAC
6121231 TCGTCAATAATTTATCAAAAATAATTCAAAGTCCAAATTAAC
1 TCGTCAATAATTTATCAAAAATAATTCAAAGTCCAAATTAAC
6121273 T
1 T
6121274 TGAAAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (42 bp):
TCGTCAATAATTTATCAAAAATAATTCAAAGTCCAAATTAAC
Found at i:6134706 original size:17 final size:17
Alignment explanation
Indices: 6134666--6134716 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
6134656 TTAAGAATTT
*
6134666 ATTTAAAAAATAAAAATA
1 ATTTTAAAAA-AAAAATA
**
6134684 ATTTTATTAAAAAAAT-
1 ATTTTAAAAAAAAAATA
6134700 ATATTTAAAAAAAAAAT
1 AT-TTTAAAAAAAAAAT
6134717 TCAAAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 2 0.07
17 18 0.67
18 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTTTAAAAAAAAAATA
Found at i:6135131 original size:7 final size:7
Alignment explanation
Indices: 6135121--6135173 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
6135111 TATTTTTTAT
6135121 TTTTTCC
1 TTTTTCC
6135128 TTTTTCC
1 TTTTTCC
6135135 TTTTTCC
1 TTTTTCC
6135142 TTTTTCC
1 TTTTTCC
6135149 TTTTTCC
1 TTTTTCC
6135156 TTTTTCC
1 TTTTTCC
6135163 TTTTTCC
1 TTTTTCC
6135170 TTTT
1 TTTT
6135174 AAAAATAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCC
Found at i:6136693 original size:31 final size:32
Alignment explanation
Indices: 6136651--6136724 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 32
6136641 TTAAAACTTA
* *
6136651 CAATATAGTCCCCCAACATTTAGTCTGTTT-T
1 CAATATGGTCCCCCAACATTTAGTCCGTTTGT
6136682 CAATATGGTCCCCCAACATTTAGTCCGTTTGT
1 CAATATGGTCCCCCAACATTTAGTCCGTTTGT
6136714 -AATATGGTCCC
1 CAATATGGTCCC
6136725 GAAGTAACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (32 bp):
CAATATGGTCCCCCAACATTTAGTCCGTTTGT
Found at i:6138072 original size:31 final size:30
Alignment explanation
Indices: 6138034--6138110 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
6138024 CTTTTAAAAC
* *
6138034 TTGCAATATAGTCCCACAACATTTAGTTCGT
1 TTGCAATAT-GTCCCACAAAATTTAGTTCAT
* * *
6138065 TTTCAATATGATCCCCCAAAATTTAGTTTAT
1 TTGCAATATG-TCCCACAAAATTTAGTTCAT
6138096 TTGCAATATGGTCCC
1 TTGCAATAT-GTCCC
6138111 TGATGTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 36 0.95
32 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (30 bp):
TTGCAATATGTCCCACAAAATTTAGTTCAT
Found at i:6139732 original size:9 final size:9
Alignment explanation
Indices: 6139720--6139752 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
6139710 ATGATAATGT
6139720 TGATGAAGA
1 TGATGAAGA
6139729 TGATGAAGA
1 TGATGAAGA
*
6139738 TGATGACGA
1 TGATGAAGA
6139747 TGATGA
1 TGATGA
6139753 TGATATGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.03, G:0.33, T:0.24
Consensus pattern (9 bp):
TGATGAAGA
Found at i:6141538 original size:2 final size:2
Alignment explanation
Indices: 6141533--6141565 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6141523 ACTGCCTGCT
6141533 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6141566 TCCCGTGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6142731 original size:14 final size:14
Alignment explanation
Indices: 6142712--6142739 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6142702 GCAGAACAGC
6142712 TCTCTCTCTTTCTT
1 TCTCTCTCTTTCTT
6142726 TCTCTCTCTTTCTT
1 TCTCTCTCTTTCTT
6142740 CACATTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTCTCTCTTTCTT
Found at i:6146681 original size:3 final size:3
Alignment explanation
Indices: 6146673--6146747 Score: 100
Period size: 3 Copynumber: 25.3 Consensus size: 3
6146663 TTAATATACT
* * *
6146673 TAA TAA TAA TAA CAA TAA TAA TAA TAA CAA TAA CAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
6146722 -AA T-A TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6146748 TAACACCGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.89
4 3 0.05
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6157206 original size:24 final size:24
Alignment explanation
Indices: 6157179--6157285 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
6157169 AAACGGAGAT
*
6157179 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
6157203 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
6157227 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
6157251 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
6157275 ATCAGAAATCA
1 ATCAGAAATCA
6157286 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:6157285 original size:48 final size:48
Alignment explanation
Indices: 6157179--6157287 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
6157169 AAACGGAGAT
* * * *
6157179 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
6157227 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
6157275 ATCAGAAATCAGA
1 ATCAGAAATCAGA
6157288 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:6159754 original size:7 final size:7
Alignment explanation
Indices: 6159742--6159773 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
6159732 TGGTCAACTC
6159742 CGGTCAA
1 CGGTCAA
6159749 CGGTCAA
1 CGGTCAA
6159756 CGGGTCAA
1 C-GGTCAA
6159764 CGGTCAA
1 CGGTCAA
6159771 CGG
1 CGG
6159774 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:6159763 original size:8 final size:8
Alignment explanation
Indices: 6159743--6159789 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
6159733 GGTCAACTCC
6159743 GGTCAAC-
1 GGTCAACG
6159750 GGTCAACG
1 GGTCAACG
6159758 GGTCAAC-
1 GGTCAACG
6159765 GGTCAACG
1 GGTCAACG
6159773 GGT---CG
1 GGTCAACG
6159778 GGTCAACG
1 GGTCAACG
6159786 GGTC
1 GGTC
6159790 GGGTCGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:6159763 original size:15 final size:15
Alignment explanation
Indices: 6159743--6159789 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
6159733 GGTCAACTCC
6159743 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
6159758 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
6159773 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
6159786 GGTC
1 GGTC
6159790 GGGTCGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:6159783 original size:13 final size:13
Alignment explanation
Indices: 6159750--6159794 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
6159740 TCCGGTCAAC
*
6159750 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
6159765 GGTCAACGGGTCG
1 GGTCAACGGGTCG
6159778 GGTCAACGGGTCG
1 GGTCAACGGGTCG
6159791 GGTC
1 GGTC
6159795 GGGTAAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:6159794 original size:18 final size:18
Alignment explanation
Indices: 6159771--6159833 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
6159761 CAACGGTCAA
6159771 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* *
6159789 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTCAACGGGT
6159807 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
6159825 -GGGTCGGGT
1 CGGGTCGGGT
6159834 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 9 0.22
18 32 0.78
ACGTcount: A:0.11, C:0.17, G:0.52, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:6162009 original size:25 final size:24
Alignment explanation
Indices: 6161980--6162045 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 24
6161970 ATAATTCAGA
6161980 TCAGATCAGATATCAGAACAGAATT
1 TCAGATCAGATATCAGAACAGAA-T
* *
6162005 TCAGATCAGATGTCAAAACAGAAT
1 TCAGATCAGATATCAGAACAGAAT
* *
6162029 TCAAATCAGAAATCAGA
1 TCAGATCAGATATCAGA
6162046 TGTAAAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 14 0.40
25 21 0.60
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
TCAGATCAGATATCAGAACAGAAT
Found at i:6162014 original size:13 final size:13
Alignment explanation
Indices: 6161979--6162046 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 13
6161969 CATAATTCAG
6161979 ATCAGATCAG-AT
1 ATCAGATCAGAAT
*
6161991 ATCAGAACAGAAT
1 ATCAGATCAGAAT
*
6162004 TTCAGATCAG-AT
1 ATCAGATCAGAAT
* * *
6162016 GTCAAAACAGAAT
1 ATCAGATCAGAAT
*
6162029 -TCAAATCAGAA-
1 ATCAGATCAGAAT
6162040 ATCAGAT
1 ATCAGAT
6162047 GTAAAATATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
12 33 0.73
13 12 0.27
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (13 bp):
ATCAGATCAGAAT
Found at i:6164485 original size:7 final size:7
Alignment explanation
Indices: 6164473--6164504 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
6164463 TGGTCAACTC
6164473 CGGTCAA
1 CGGTCAA
6164480 CGGTCAA
1 CGGTCAA
6164487 CGGGTCAA
1 C-GGTCAA
6164495 CGGTCAA
1 CGGTCAA
6164502 CGG
1 CGG
6164505 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:6164494 original size:8 final size:8
Alignment explanation
Indices: 6164474--6164520 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
6164464 GGTCAACTCC
6164474 GGTCAAC-
1 GGTCAACG
6164481 GGTCAACG
1 GGTCAACG
6164489 GGTCAAC-
1 GGTCAACG
6164496 GGTCAACG
1 GGTCAACG
6164504 GGT---CG
1 GGTCAACG
6164509 GGTCAACG
1 GGTCAACG
6164517 GGTC
1 GGTC
6164521 GGGTCGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:6164494 original size:15 final size:15
Alignment explanation
Indices: 6164474--6164520 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
6164464 GGTCAACTCC
6164474 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
6164489 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
6164504 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
6164517 GGTC
1 GGTC
6164521 GGGTCGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:6164514 original size:13 final size:13
Alignment explanation
Indices: 6164481--6164525 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
6164471 TCCGGTCAAC
*
6164481 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
6164496 GGTCAACGGGTCG
1 GGTCAACGGGTCG
6164509 GGTCAACGGGTCG
1 GGTCAACGGGTCG
6164522 GGTC
1 GGTC
6164526 GGGTAAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:6164525 original size:18 final size:18
Alignment explanation
Indices: 6164502--6164565 Score: 110
Period size: 18 Copynumber: 3.6 Consensus size: 18
6164492 CAACGGTCAA
6164502 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* *
6164520 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTCAACGGGT
6164538 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
6164556 CGGGTCGGGT
1 CGGGTCGGGT
6164566 TGTGACCGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.11, C:0.19, G:0.52, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:6165671 original size:25 final size:26
Alignment explanation
Indices: 6165630--6165680 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
6165620 GATGATGATG
*
6165630 ATAATATTTTATAA-TTTAAAAAATT
1 ATAATATTTCATAATTTTAAAAAATT
*
6165655 ATAA-ATTTCATATATTTTTAAAAATT
1 ATAATATTTCATA-ATTTTAAAAAATT
6165681 TATTGACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAATATTTCATAATTTTAAAAAATT
Found at i:6165935 original size:20 final size:21
Alignment explanation
Indices: 6165912--6165972 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
6165902 TTAGCTTTAC
6165912 ATTCTA-TTTTATTGAATTTT
1 ATTCTACTTTTATTGAATTTT
*
6165932 ATTC-ACTTTTAATT-ATTTTT
1 ATTCTACTTTT-ATTGAATTTT
* * *
6165952 ATTGTATTTTTATTGATTTTT
1 ATTCTACTTTTATTGAATTTT
6165973 TAAAAAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 19 0.56
21 14 0.41
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTCTACTTTTATTGAATTTT
Found at i:6165974 original size:11 final size:10
Alignment explanation
Indices: 6165918--6165972 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 10
6165908 TTACATTCTA
*
6165918 TTTTATTGAA
1 TTTTATTGAT
*
6165928 TTTTATTCACT
1 TTTTATTGA-T
*
6165939 TTTAATT-AT
1 TTTTATTGAT
6165948 TTTTATTGTAT
1 TTTTATTG-AT
6165959 TTTTATTGAT
1 TTTTATTGAT
6165969 TTTT
1 TTTT
6165973 TAAAAAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 7 0.18
10 15 0.39
11 16 0.42
ACGTcount: A:0.22, C:0.04, G:0.05, T:0.69
Consensus pattern (10 bp):
TTTTATTGAT
Found at i:6170940 original size:24 final size:24
Alignment explanation
Indices: 6170913--6171022 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
6170903 GTAAACGGAG
*
6170913 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
6170937 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
6170961 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
6170984 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
6171008 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
6171023 TAAAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.23
24 50 0.71
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:6170944 original size:12 final size:12
Alignment explanation
Indices: 6170917--6171008 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
6170907 ACGGAGATAT
* *
6170917 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
6170929 CAGAATTCATAT
1 CAGAATTCAGAA
6170941 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
6170953 CAGAATCCAGAT
1 CAGAATTCAGAA
6170965 CAGAA-TCAGAA
1 CAGAATTCAGAA
6170976 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
6170990 C-GTA-TCAGAA
1 CAGAATTCAGAA
6171000 CAGAATTCA
1 CAGAATTCA
6171009 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:6170996 original size:47 final size:48
Alignment explanation
Indices: 6170915--6171005 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
6170905 AAACGGAGAT
*
6170915 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
6170963 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
6171006 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:6172127 original size:18 final size:18
Alignment explanation
Indices: 6172106--6172140 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6172096 TGTCATCCGG
*
6172106 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
6172124 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
6172141 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:6175472 original size:104 final size:104
Alignment explanation
Indices: 6175226--6175476 Score: 322
Period size: 104 Copynumber: 2.4 Consensus size: 104
6175216 AAGTGACAAG
* * * * * *
6175226 ATATATGTCATGTTATCACTATAAGTTATGCGACACAGACTACGTCATCAAATTTAGTTATGTGA
1 ATATAT-T-ATGTCATCACTTTAAGTAATGCGACACATACTACGTCATCAAATTTAGTAACGTGA
* * **
6175291 TACGTGTCATGTTTTCACCTTGGATCTTTGAGTTACATGAC
64 CACGTGTCATGTCTTCACCTTAAATCTTTGAGTTACATGAC
* * * * *
6175332 ATATATAATGTCATCAGTTTGAGTGATGCGATACATACTACGTCATCAAATTTAGTAACGTGACA
1 ATATATTATGTCATCACTTTAAGTAATGCGACACATACTACGTCATCAAATTTAGTAACGTGACA
*
6175397 TGTGTCATGTCTTCACCTTAAATCTTTGAGTTACATGAC
66 CGTGTCATGTCTTCACCTTAAATCTTTGAGTTACATGAC
* *
6175436 ATATATTATGTCATCACTTTAAGTAACGCAACACATACTAC
1 ATATATTATGTCATCACTTTAAGTAATGCGACACATACTAC
6175477 TGTGTCATGT
Statistics
Matches: 123, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
104 117 0.95
106 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (104 bp):
ATATATTATGTCATCACTTTAAGTAATGCGACACATACTACGTCATCAAATTTAGTAACGTGACA
CGTGTCATGTCTTCACCTTAAATCTTTGAGTTACATGAC
Found at i:6182532 original size:20 final size:21
Alignment explanation
Indices: 6182503--6182541 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
6182493 ATATAAAAAT
6182503 ATATATTTTTGA-ATAAATGAA
1 ATATATTTTT-ACATAAATGAA
6182524 ATATA-TTTTACATAAATG
1 ATATATTTTTACATAAATG
6182542 TTTAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 11 0.65
21 5 0.29
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (21 bp):
ATATATTTTTACATAAATGAA
Found at i:6189599 original size:19 final size:19
Alignment explanation
Indices: 6189575--6189611 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6189565 ATGACCAACA
* *
6189575 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
6189594 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
6189612 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:6189699 original size:20 final size:20
Alignment explanation
Indices: 6189641--6189700 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
6189631 CCAGATTCGT
*
6189641 AACGCGATTTTGACTATCGC
1 AACGCGATTATGACTATCGC
* * *
6189661 AATGCGAATATGTA-AATCGC
1 AACGCGATTATG-ACTATCGC
*
6189681 AACGCGATTCTGACTATCGC
1 AACGCGATTATGACTATCGC
6189701 GTTGCGATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
AACGCGATTATGACTATCGC
Found at i:6189923 original size:22 final size:22
Alignment explanation
Indices: 6189875--6189924 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
6189865 CTACGATGAC
*
6189875 ATCCATCCCCATCTCCAACGAA
1 ATCCGTCCCCATCTCCAACGAA
* **
6189897 ATCCGTCCCTATCTCCGGCGAA
1 ATCCGTCCCCATCTCCAACGAA
6189919 ATCCGT
1 ATCCGT
6189925 TTATCTCCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.42, G:0.12, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAACGAA
Found at i:6190329 original size:20 final size:20
Alignment explanation
Indices: 6190300--6190343 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6190290 GCGATTTTAG
6190300 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
6190320 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
6190340 TTTC
1 TTTC
6190344 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:6190871 original size:20 final size:20
Alignment explanation
Indices: 6190835--6190886 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
6190825 GGTAACTTTT
*
6190835 GCAACGCTAAA-CTCAAAATC
1 GCAACGCGAAAGC-CAAAATC
*
6190855 GCAATGCGAAAGCCAAAATC
1 GCAACGCGAAAGCCAAAATC
6190875 GCAACGCGAAAG
1 GCAACGCGAAAG
6190887 TCAATTCGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.27, G:0.19, T:0.10
Consensus pattern (20 bp):
GCAACGCGAAAGCCAAAATC
Found at i:6190902 original size:19 final size:20
Alignment explanation
Indices: 6190880--6190922 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
6190870 AAATCGCAAC
*
6190880 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
6190899 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
6190919 GCGA
1 GCGA
6190923 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:6190959 original size:20 final size:20
Alignment explanation
Indices: 6190931--6190985 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
6190921 GATTTTCTCG
*
6190931 TTGCGATAGTCAAATTCGCA
1 TTGCAATAGTCAAATTCGCA
*
6190951 TTGCAATAGTCAAATTCGCG
1 TTGCAATAGTCAAATTCGCA
*
6190971 TTGCAATATTCAAAT
1 TTGCAATAGTCAAAT
6190986 GAATGTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
TTGCAATAGTCAAATTCGCA
Found at i:6191179 original size:18 final size:18
Alignment explanation
Indices: 6191156--6191190 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6191146 AAGCCGGTTG
*
6191156 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
6191174 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
6191191 GTCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:6193484 original size:24 final size:24
Alignment explanation
Indices: 6193450--6193503 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6193440 CTGAAACATC
6193450 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
6193474 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
6193498 ATCAAA
1 ATCAAA
6193504 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:6193517 original size:24 final size:24
Alignment explanation
Indices: 6193450--6193517 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
6193440 CTGAAACATC
* * *
6193450 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
6193474 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
6193498 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
6193518 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:6194790 original size:31 final size:31
Alignment explanation
Indices: 6194731--6194805 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
6194721 TAAATTAATT
* * *
6194731 TTAATTTATTCTTTTAAAATTTAGATAAAATA
1 TTAATTTAAT-TTTTAAAATTTAAATAAAACA
*
6194763 TTAATTTAATTTTTAAATTTTAAATAAAACA
1 TTAATTTAATTTTTAAAATTTAAATAAAACA
*
6194794 TCAATTTAATTT
1 TTAATTTAATTT
6194806 CTGAATTCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 29 0.76
32 9 0.24
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (31 bp):
TTAATTTAATTTTTAAAATTTAAATAAAACA
Found at i:6199198 original size:21 final size:20
Alignment explanation
Indices: 6199174--6199220 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
6199164 AAAATGAATT
6199174 AAAAAATTTACTT-AAAAATCC
1 AAAAAA-TT-CTTAAAAAATCC
*
6199195 AAAATAATTCTTAAAAAATCT
1 AAAA-AATTCTTAAAAAATCC
6199216 AAAAA
1 AAAAA
6199221 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 17 0.74
22 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAATTCTTAAAAAATCC
Found at i:6199230 original size:20 final size:20
Alignment explanation
Indices: 6199207--6199245 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6199197 AATAATTCTT
* *
6199207 AAAAAATCTAAAAATTAATA
1 AAAAAACCTAAAAACTAATA
*
6199227 AAAATACCTAAAAACTAAT
1 AAAAAACCTAAAAACTAAT
6199246 TTTAAAGAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAACCTAAAAACTAATA
Found at i:6210719 original size:35 final size:35
Alignment explanation
Indices: 6210673--6210748 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
6210663 GCAAAAAACC
* *
6210673 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** *
6210708 TCAATTTCATTCTAAACCTTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
6210743 TCAATT
1 TCAATT
6210749 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:6211298 original size:130 final size:129
Alignment explanation
Indices: 6211124--6211370 Score: 386
Period size: 130 Copynumber: 1.9 Consensus size: 129
6211114 TTATTATATA
* **
6211124 ATCAATTTGATCCTAAATTAAATAGAATTAATAAATTAATCATTTAATTAGGATCTGACATATGT
1 ATCAATTTGATCCTAAATTAAATAAAATTAATAAATTAATCATTTAACCAGGATCTGACATATGT
* *
6211189 TAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACAACCTAATTATTTATATATGCT
66 TAACACATGATCATGACACATGTCATTGGTGACACATGTCACAACCTAATTATTTATATATGCT
* *
6211253 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGATCCTAAATTAAATAAAA-TTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * * *
6211318 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
65 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACAACCTAATTA
6211371 GAAGAAATTA
Statistics
Matches: 106, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 25 0.24
130 81 0.76
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (129 bp):
ATCAATTTGATCCTAAATTAAATAAAATTAATAAATTAATCATTTAACCAGGATCTGACATATGT
TAACACATGATCATGACACATGTCATTGGTGACACATGTCACAACCTAATTATTTATATATGCT
Found at i:6211851 original size:15 final size:16
Alignment explanation
Indices: 6211827--6211863 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6211817 TTTAATTTCT
6211827 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
6211841 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
6211857 TGATTCA
1 T-ATTCA
6211864 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:6213855 original size:5 final size:5
Alignment explanation
Indices: 6213845--6213890 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
6213835 AGATAACTTA
6213845 CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC C
1 CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC CGCTC C
6213891 ATCCTATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.00, C:0.61, G:0.20, T:0.20
Consensus pattern (5 bp):
CGCTC
Found at i:6216023 original size:16 final size:16
Alignment explanation
Indices: 6216002--6216048 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
6215992 ACTTAGGTAA
6216002 TTTTAAAAATTTTATT
1 TTTTAAAAATTTTATT
* *
6216018 TTTTAAAAAATATAATT
1 TTTT-AAAAATTTTATT
6216035 TTTT-AAAATTTTAT
1 TTTTAAAAATTTTAT
6216049 AAAGACAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAAATTTTATT
Found at i:6222307 original size:59 final size:58
Alignment explanation
Indices: 6222235--6222402 Score: 187
Period size: 59 Copynumber: 2.9 Consensus size: 58
6222225 ATTATAATTC
* * * * *
6222235 TCATTTTAAATTAGTCCTTAAATTTTTTAATATTCCAATTTCATTCCTAAGCTATGACT
1 TCATTTTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCA-TCCCAAACTATGACT
*
6222294 TCATTTTAAATTAGTCCTTAAACTTTTGAACATTCCATTTTCATCCCAAACTATGACT
1 TCATTTTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCAAACTATGACT
* * ** *
6222352 CTCACTATAAATT-GATCCCCAAACTTTTGAATC-TTTCAATTTCATCCCAAA
1 -TCATTTTAAATTAG-TCCTTAAACTTTTGAA-CATTCCAATTTCATCCCAAA
6222403 ATCATCCAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 14 0.15
59 79 0.84
60 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (58 bp):
TCATTTTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCAAACTATGACT
Found at i:6224032 original size:21 final size:21
Alignment explanation
Indices: 6224006--6224054 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
6223996 AGTGCCCAAC
6224006 AATAATAAAACCGGTAGAAAA
1 AATAATAAAACCGGTAGAAAA
* *
6224027 AATAATTAAACCGGTAGAAAT
1 AATAATAAAACCGGTAGAAAA
6224048 AATAATA
1 AATAATA
6224055 TTTTAGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (21 bp):
AATAATAAAACCGGTAGAAAA
Found at i:6226262 original size:12 final size:12
Alignment explanation
Indices: 6226245--6226283 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
6226235 GACCCTCAAG
6226245 AAATAGAGAAGA
1 AAATAGAGAAGA
6226257 AAATAGAAGAAGA
1 AAATAG-AGAAGA
*
6226270 AGA-AGAGAAGA
1 AAATAGAGAAGA
6226281 AAA
1 AAA
6226284 GATAGAGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 8 0.33
13 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (12 bp):
AAATAGAGAAGA
Found at i:6233744 original size:29 final size:29
Alignment explanation
Indices: 6233702--6233758 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
6233692 AGTGTTGGCC
*
6233702 GTAGGTCGTCATGCACTCCAGGCGACCTT
1 GTAGGTCGCCATGCACTCCAGGCGACCTT
*
6233731 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCAGGCGACCT
6233759 ACCCTTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCAGGCGACCTT
Found at i:6233872 original size:29 final size:29
Alignment explanation
Indices: 6233826--6233881 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
6233816 ACCCAACACA
*
6233826 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
6233855 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
6233882 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:6234013 original size:29 final size:29
Alignment explanation
Indices: 6233980--6234035 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
6233970 GCAATCTCTT
*
6233980 GTAGGTCA-CCGGGAAGACATGGCGACCTA
1 GTAGGTCACCCGGAAAG-CATGGCGACCTA
*
6234009 GTAGGTCTCCCGGAAAGCATGGCGACC
1 GTAGGTCACCCGGAAAGCATGGCGACC
6234036 AACGGCCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGGTCACCCGGAAAGCATGGCGACCTA
Found at i:6237096 original size:21 final size:20
Alignment explanation
Indices: 6237016--6237097 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 20
6237006 CGCAAATCAG
*
6237016 TTTCCAGATTCGCAACGCGAT
1 TTTCCA-ATTCGCAATGCGAT
**
6237037 TATGACAA-TCGCAATGCGAT
1 T-TTCCAATTCGCAATGCGAT
* **
6237057 TTTCCAATTTTGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
6237078 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
6237098 ATAAGTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.09
20 12 0.26
21 23 0.50
22 7 0.15
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:6237112 original size:20 final size:21
Alignment explanation
Indices: 6237087--6237138 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6237077 TTTTCCCAAT
*
6237087 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
6237107 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
6237128 TCGCAATGCGA
1 TCGCAATGCGA
6237139 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6237117 original size:41 final size:41
Alignment explanation
Indices: 6237072--6237321 Score: 186
Period size: 41 Copynumber: 6.1 Consensus size: 41
6237062 AATTTTGCGT
** * *
6237072 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATACGTAAATCGCAA
* * * *
6237113 TGCGAATTTGGAAAATCGCAATGCG-ATAC-TGACTATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATACGT-A-AATCGCAA
** * * * * * **
6237154 TGTAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCGTAAATCGCAATGCGA-ATACGTAAATCGCAA
* * *
6237195 TGCGATTTTCATAATTCGCAATACGAATACGTAAATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATACGTAAATCGCAA
* ** * *
6237236 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAA-TACGTAAATCGCAA
* *
6237277 TGCGA-ATACGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATACGTAAATCGCAA
6237317 TGCGA
1 TGCGA
6237322 ATCTTACTAT
Statistics
Matches: 160, Mismatches: 42, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
39 1 0.01
40 42 0.26
41 113 0.71
43 3 0.02
44 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (41 bp):
TGCGATTTTCGTAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:6237182 original size:21 final size:21
Alignment explanation
Indices: 6237158--6237214 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
6237148 TCGCAATGTA
*
6237158 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
6237179 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
6237199 ATTTTCATAATTCGCA
1 ATTTTCATAATTCGCA
6237215 ATACGAATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:6237235 original size:20 final size:20
Alignment explanation
Indices: 6237210--6237341 Score: 167
Period size: 20 Copynumber: 6.5 Consensus size: 20
6237200 TTTTCATAAT
*
6237210 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
6237230 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
6237250 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
6237271 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
6237291 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
6237311 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
6237331 TCGCAATGCGA
1 TCGCAATGCGA
6237342 TTTACATAGC
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
19 3 0.03
20 77 0.79
21 18 0.18
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:6237608 original size:27 final size:27
Alignment explanation
Indices: 6237551--6237603 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
6237541 CATCGCCGGC
* *
6237551 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
6237578 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
6237604 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:6237937 original size:19 final size:19
Alignment explanation
Indices: 6237898--6237939 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6237888 GCAACGAGAG
* **
6237898 AATCGCAACGCGAAATGAA
1 AATCACAACGCGAAACCAA
6237917 AATCACAACGCGAAACCAA
1 AATCACAACGCGAAACCAA
6237936 AATC
1 AATC
6237940 GCGTTGCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.26, G:0.14, T:0.10
Consensus pattern (19 bp):
AATCACAACGCGAAACCAA
Found at i:6238041 original size:20 final size:19
Alignment explanation
Indices: 6237955--6238064 Score: 104
Period size: 20 Copynumber: 5.9 Consensus size: 19
6237945 GCGATTCTCT
*
6237955 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
*
6237974 CGTTGCGATAGTCATTTCG
1 CGTTGCGATATTCATTTCG
*
6237993 CGTTGC-A-ATTC---TCT
1 CGTTGCGATATTCATTTCG
*
6238007 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATATTCATTT-CG
* *
6238027 CGTTGCGATTTTCATTATCT
1 CGTTGCGATATTCATT-TCG
*
6238047 CGTTGCGATTTTCATTTC
1 CGTTGCGATATTCATTTC
6238065 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 8 0.11
15 1 0.01
16 3 0.04
17 3 0.04
18 1 0.01
19 26 0.35
20 32 0.43
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:6240270 original size:21 final size:20
Alignment explanation
Indices: 6240211--6240271 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
6240201 CTCGAGCGTC
6240211 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
6240231 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
6240252 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
6240272 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:6241641 original size:14 final size:14
Alignment explanation
Indices: 6241622--6241657 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6241612 ATTGTTTAAT
6241622 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
6241636 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
6241650 TGATTTGT
1 TGATTTGT
6241658 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:6241786 original size:19 final size:19
Alignment explanation
Indices: 6241764--6241874 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 19
6241754 AAAAATTACT
6241764 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6241783 ATCGCAA--CG--AT-ATA
1 ATCGCAATGCGAAATGAAA
6241797 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
6241816 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
6241830 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6241849 ATCGCAACGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
6241868 ATCGCAA
1 ATCGCAA
6241875 CACGAAACTA
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
14 19 0.26
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 40 0.54
20 1 0.01
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6241806 original size:33 final size:33
Alignment explanation
Indices: 6241764--6241857 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
6241754 AAAAATTACT
* *
6241764 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
6241797 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
6241830 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
6241858 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:6241875 original size:19 final size:19
Alignment explanation
Indices: 6241846--6241891 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
6241836 ATGCGAAATG
*
6241846 AAAATCGCAACGCGAAACT
1 AAAATCGCAACACGAAACT
6241865 AAAATCGCAACACGAAACT
1 AAAATCGCAACACGAAACT
*
6241884 AAATTCGC
1 AAAATCGC
6241892 GATGCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACACGAAACT
Found at i:6241936 original size:33 final size:33
Alignment explanation
Indices: 6241894--6242017 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
6241884 AAATTCGCGA
*
6241894 TGCGATTTTCATTTCGCTTTGCGATTTCCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTCCTCGT
6241927 TGCGATTTTCATTTCGCATTGCGA-TTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTC-CTCGT
*
6241960 TGCGATTTTCATTTCGCATTGCAATTAT-CTCGT
1 TGCGATTTTCATTTCGCATTGCGATT-TCCTCGT
6241993 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
6242018 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
32 3 0.04
33 80 0.94
34 1 0.01
35 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTCCTCGT
Found at i:6241950 original size:19 final size:19
Alignment explanation
Indices: 6241894--6242037 Score: 102
Period size: 19 Copynumber: 8.3 Consensus size: 19
6241884 AAATTCGCGA
*
6241894 TGCGATTTTCATTTCGCTT
1 TGCGATTTTCATTTCGCAT
*
6241913 TGCGA-TTTC--CTCG--T
1 TGCGATTTTCATTTCGCAT
6241927 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
*
6241946 TGCGA--TTC-TCTCG--T
1 TGCGATTTTCATTTCGCAT
6241960 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
* *
6241979 TGC-A-ATT-ATCTCG--T
1 TGCGATTTTCATTTCGCAT
6241993 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
** *
6242012 TGCGATAGTAATTTCCGCAT
1 TGCGATTTTCATTT-CGCAT
6242032 TGCGAT
1 TGCGAT
6242038 AGACATTAAG
Statistics
Matches: 98, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
14 16 0.16
15 5 0.05
16 17 0.17
17 17 0.17
18 5 0.05
19 27 0.28
20 11 0.11
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAT
Found at i:6242083 original size:20 final size:20
Alignment explanation
Indices: 6242011--6242083 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
6242001 TCATTTCGCA
* **
6242011 TTGCGATAGTAATTTCCGCA
1 TTGCGATAGTCATTTCCGTG
* **
6242031 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
6242051 ATTGCGA-ATGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
6242072 TTGCGATAGTCA
1 TTGCGATAGTCA
6242084 AATGATTGCC
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
19 3 0.08
20 21 0.54
21 12 0.31
22 3 0.08
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:6245082 original size:41 final size:42
Alignment explanation
Indices: 6245028--6245117 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 42
6245018 CCTCTTCAAC
* * *
6245028 GATGACAGTGGCCTCTTAAAC-GGTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTAAACAAGTGGAGGGGACTCTTGAGG
* * *
6245069 GATGATAGGGGCCTCTTGAACAATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTAAACAAGTGGAGGGGACTCTTGAGG
*
6245111 AATGACA
1 GATGACA
6245118 TGTGAGTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 18 0.45
42 22 0.55
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTAAACAAGTGGAGGGGACTCTTGAGG
Found at i:6245482 original size:20 final size:20
Alignment explanation
Indices: 6245457--6245529 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
6245447 GAAGAATAGT
*
6245457 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
6245477 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
6245497 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
6245517 TGACTATCGCAAC
1 TTACTTTCGCAAC
6245530 GCGGAAATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:6245507 original size:40 final size:40
Alignment explanation
Indices: 6245463--6245544 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
6245453 TAGTTTACTT
* *
6245463 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* *
6245503 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGACTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
6245543 TC
1 TC
6245545 ACAATGCGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 33 0.89
41 4 0.11
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:6245530 original size:20 final size:20
Alignment explanation
Indices: 6245483--6245569 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
6245473 AAACTTACTT
*
6245483 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
6245503 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
6245523 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
* * **
6245543 TCACAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
6245562 TCGCAACG
1 TCGCAACG
6245570 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:6245577 original size:14 final size:14
Alignment explanation
Indices: 6245558--6245616 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
6245548 ATGCGAAATG
6245558 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
6245572 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
6245591 AAAATCGCAACGAT
1 AAAATCGCAACGAC
6245605 AAAATCGCAACG
1 AAAATCGCAACG
6245617 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Done.