Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009953.1 Kokia drynarioides strain JFW-HI SEQ_124698, 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: 113026
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:419 original size:17 final size:18
Alignment explanation
Indices: 397--430 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
387 ATAATAATTA
397 TGAAGATTTTGG-ATATG
1 TGAAGATTTTGGCATATG
414 TGAAGATTTTGGCATAT
1 TGAAGATTTTGGCATAT
431 TCCCCGAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (18 bp):
TGAAGATTTTGGCATATG
Found at i:11879 original size:17 final size:17
Alignment explanation
Indices: 11849--11888 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
11839 TATATTTTTT
11849 TAAAA-ATTAAAAAAAA
1 TAAAATATTAAAAAAAA
* *
11865 TCAAATATTACAAAAAA
1 TAAAATATTAAAAAAAA
11882 TAAAATA
1 TAAAATA
11889 ACAAGGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAAATATTAAAAAAAA
Found at i:12164 original size:50 final size:50
Alignment explanation
Indices: 12109--12243 Score: 125
Period size: 49 Copynumber: 2.7 Consensus size: 50
12099 TATTTTTTCT
12109 CTAATTAATTTAAAGTAATTAAGAGATAAATAATAAAAAATTACATTAT-A
1 CTAATTAA-TTAAAGTAATTAAGAGATAAATAATAAAAAATTACATTATCA
* * * * ** ** *
12159 CTAATTAAAATAAAATAATTAAGTGAT-AATATTAAATGATTATTTTATCT
1 CTAATT-AATTAAAGTAATTAAGAGATAAATAATAAAAAATTACATTATCA
*
12209 CTAATTAATT-AAGTTAA-TAAGAGATAAATACTAAA
1 CTAATTAATTAAAG-TAATTAAGAGATAAATAATAAA
12244 TAAAAGAGTT
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
48 9 0.13
49 30 0.44
50 27 0.40
51 2 0.03
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (50 bp):
CTAATTAATTAAAGTAATTAAGAGATAAATAATAAAAAATTACATTATCA
Found at i:14610 original size:25 final size:27
Alignment explanation
Indices: 14555--14610 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
14545 TAAACATTAA
* *
14555 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAAATTAATATTAAGAAAATCACT
*
14582 -TTAAAATTAA-ATTAATAAAAT-ACT
1 ATTAAAATTAATATTAAGAAAATCACT
14606 ATTAA
1 ATTAA
14611 GATAAGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (27 bp):
ATTAAAATTAATATTAAGAAAATCACT
Found at i:20400 original size:24 final size:24
Alignment explanation
Indices: 20342--20529 Score: 112
Period size: 24 Copynumber: 7.7 Consensus size: 24
20332 TTTATTGCGT
* * * *
20342 TTTACGCTCGCCAACTTTCATATG
1 TTTATGCTCGTCAGCTTTCATACG
* *
20366 TTTACGCTCGTTAGCTTTCATACG
1 TTTATGCTCGTCAGCTTTCATACG
* *
20390 TTTATGCTCGTCAG-TTTGCACACT
1 TTTATGCTCGTCAGCTTT-CATACG
*
20414 TTTATGCTCGTCAGCTATAT-ATGCG
1 TTTATGCTCGTCAGCT-T-TCATACG
* * * * *
20439 TTTACGCTCGCCAGCTTGCACACA
1 TTTATGCTCGTCAGCTTTCATACG
20463 TTTATGCTCGTCAGCTTAT-ATATGCG
1 TTTATGCTCGTCAGCTT-TCATA--CG
* * * * * *
20489 TTTACGCTTGCCAACTTGCACACG
1 TTTATGCTCGTCAGCTTTCATACG
*
20513 TTTATGCTCATCAGCTT
1 TTTATGCTCGTCAGCTT
20530 ATATATATAT
Statistics
Matches: 122, Mismatches: 33, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
23 3 0.02
24 84 0.69
25 17 0.14
26 17 0.14
27 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (24 bp):
TTTATGCTCGTCAGCTTTCATACG
Found at i:20507 original size:50 final size:50
Alignment explanation
Indices: 20337--20535 Score: 217
Period size: 50 Copynumber: 4.0 Consensus size: 50
20327 ACATGTTTAT
* * ** * *
20337 TGCGTTTTACGCTCGCCAACTTTCATATGTTTACGCTCGTTAGCTT-TCATA
1 TGCG-TTTACGCTCGCCAACTTGCACACATTTATGCTCGTCAGCTTAT-ATA
* * ** *
20388 --CGTTTATGCTCGTCAGTTTGCACACTTTTATGCTCGTCAGC-TATATA
1 TGCGTTTACGCTCGCCAACTTGCACACATTTATGCTCGTCAGCTTATATA
*
20435 TGCGTTTACGCTCGCCAGCTTGCACACATTTATGCTCGTCAGCTTATATA
1 TGCGTTTACGCTCGCCAACTTGCACACATTTATGCTCGTCAGCTTATATA
* * *
20485 TGCGTTTACGCTTGCCAACTTGCACACGTTTATGCTCATCAGCTTATATA
1 TGCGTTTACGCTCGCCAACTTGCACACATTTATGCTCGTCAGCTTATATA
20535 T
1 T
20536 ATATATATCG
Statistics
Matches: 126, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
47 4 0.03
48 30 0.24
49 39 0.31
50 53 0.42
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (50 bp):
TGCGTTTACGCTCGCCAACTTGCACACATTTATGCTCGTCAGCTTATATA
Found at i:22197 original size:30 final size:30
Alignment explanation
Indices: 22117--22356 Score: 192
Period size: 30 Copynumber: 8.1 Consensus size: 30
22107 GAGAAATTCG
* * *
22117 AGGGTCAAAATCGAGCTTTTTGGAAA-TTTT
1 AGGGTCAAAAT-GTGATTTTTGGAAAGTTTA
* * * *
22147 GGGGTTAAAAT-TGAACTTTTGGACAAGTTCA
1 AGGGTCAAAATGTG-ATTTTTGGA-AAGTTTA
22178 AGGG-CAAAATGTGATTTTTGG-AAGTTT-
1 AGGGTCAAAATGTGATTTTTGGAAAGTTTA
* * * *
22205 GGGGCCATAATGT-ATTTTTAGAAAAAGTTTA
1 AGGGTCAAAATGTGATTTTT-G-GAAAGTTTA
* * **
22236 GGGGTTAAAATGTGATTTTAAGAAAGTTTA
1 AGGGTCAAAATGTGATTTTTGGAAAGTTTA
**
22266 AGGGTCAAAATGTGATTTAGGGAAAGTTTA
1 AGGGTCAAAATGTGATTTTTGGAAAGTTTA
* *
22296 A-GGTTAAAATGT-ATTTTGGGAAAGTTT-
1 AGGGTCAAAATGTGATTTTTGGAAAGTTTA
22323 AGAGGTCAAAATGTGATTTTTGGAAAGTTTA
1 AG-GGTCAAAATGTGATTTTTGGAAAGTTTA
22354 AGG
1 AGG
22357 ACCTTTAGTG
Statistics
Matches: 167, Mismatches: 29, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
27 10 0.06
28 28 0.17
29 27 0.16
30 78 0.47
31 19 0.11
32 5 0.03
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (30 bp):
AGGGTCAAAATGTGATTTTTGGAAAGTTTA
Found at i:22330 original size:58 final size:59
Alignment explanation
Indices: 22228--22356 Score: 181
Period size: 58 Copynumber: 2.2 Consensus size: 59
22218 ATTTTTAGAA
*
22228 AAAGTTTAGGGGTTAAAATGTGATTTTAAGAAAGTTTAAGGGTCAAAATGTGATTTAGGG
1 AAAGTTTA-AGGTTAAAATGTGATTTTAAGAAAGTTTAAGGGTCAAAATGTGATTTAGGG
** **
22288 AAAGTTTAAGGTTAAAATGT-ATTTTGGGAAAGTTT-AGAGGTCAAAATGTGATTTTTGG
1 AAAGTTTAAGGTTAAAATGTGATTTTAAGAAAGTTTAAG-GGTCAAAATGTGATTTAGGG
22346 AAAGTTTAAGG
1 AAAGTTTAAGG
22357 ACCTTTAGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
57 2 0.03
58 42 0.67
59 11 0.17
60 8 0.13
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (59 bp):
AAAGTTTAAGGTTAAAATGTGATTTTAAGAAAGTTTAAGGGTCAAAATGTGATTTAGGG
Found at i:24655 original size:208 final size:209
Alignment explanation
Indices: 24186--24673 Score: 669
Period size: 208 Copynumber: 2.3 Consensus size: 209
24176 TTCGTTGTTT
* * *
24186 TATCTCATCAGGAAGACGAATTTGATTCACTTCTCTGCATCTCATCAAGAAAATGAACACTTTAT
1 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTAT
* * *
24251 TGCTTTAACCCACTCCTCTGTATCTCATTAGGAAGATAGGGTTTGAAAGTTTCACTTATATTGAG
66 TGCTTTAACCCACTCCTCTGTACCTCATCAGGAAGATAGGGTTTGAAAGTTTCACTTACATTGAG
*
24316 CTTCACTTTGCTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTT
131 CTTCACTTTGCTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCATTGTTTT
24381 AATCCACTTCTCTG
196 AATCCACTTCTCTG
* * * * * *
24395 TATCTCATCAAGAAGACGAATTTGGTTCACTTCTTTACATCTCGTTAGGAAGATGACCAC-TTAT
1 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTAT
* * * ** * *
24459 TGGTTTGACCTACTTTTTTGTACCTCATCAGGAAGATGGGGTTTG-AAGTTTCACTTACATTGAG
66 TGCTTTAACCCACTCCTCTGTACCTCATCAGGAAGATAGGGTTTGAAAGTTTCACTTACATTGAG
* * *
24523 CTTCAC-TT-CATCGATTTGGTCTACTTCTTTGTATCTCATTAGGAAGATGACCGCATCACTTGT
131 CTTCACTTTGC-T-GAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCA-TTGT
24586 TTTAATCCACTTCTCTG
193 TTTAATCCACTTCTCTG
* * * * *
24603 TATCTCATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTAT
1 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTAT
24668 TGCTTT
66 TGCTTT
24674 GGATGACTGC
Statistics
Matches: 241, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
205 1 0.00
206 3 0.01
207 66 0.27
208 111 0.46
209 60 0.25
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (209 bp):
TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTAT
TGCTTTAACCCACTCCTCTGTACCTCATCAGGAAGATAGGGTTTGAAAGTTTCACTTACATTGAG
CTTCACTTTGCTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCATTGTTTT
AATCCACTTCTCTG
Found at i:24792 original size:39 final size:38
Alignment explanation
Indices: 24717--24806 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 38
24707 TGCAATCTGC
** *
24717 CCCATGATCGGGGTAAAAGATTGGATGACTGTAATTTAT
1 CCCATGATCGGGGTAAAAGATTGGATGACTACAATTT-G
*
24756 CCCATGATCGGGGTAAGAGATTGGATGACTACAATTTG
1 CCCATGATCGGGGTAAAAGATTGGATGACTACAATTTG
24794 CCTCATGATCGGG
1 CC-CATGATCGGG
24807 AAGATGGCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 2 0.04
39 44 0.96
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (38 bp):
CCCATGATCGGGGTAAAAGATTGGATGACTACAATTTG
Found at i:24978 original size:44 final size:42
Alignment explanation
Indices: 24821--25032 Score: 227
Period size: 41 Copynumber: 5.0 Consensus size: 42
24811 TGGCGTGTCC
* *
24821 TCAATCTGCCCTTCATGATTAGGGGTAAAAGATTGAAAT--CT
1 TCAATCTGCCC-TCTTGATTAGGGGTAAAAGATTGGAATGACT
* * *
24862 TTAATCTGCCTCTCTTGATTAGGGGTATAAGATTTGAAT--CT
1 TCAATCTGCC-CTCTTGATTAGGGGTAAAAGATTGGAATGACT
* * *
24903 TCAATATGTCCTTCTTGATTAGGGATAAAAGATTGGAATGACT
1 TCAATCTG-CCCTCTTGATTAGGGGTAAAAGATTGGAATGACT
*
24946 TCAATCTGCACCTCTTGACTTAGGGGTAAAAGATTGAAATGTA-T
1 TCAATCTGC-CCTCTTGA-TTAGGGGTAAAAGATTGGAATG-ACT
* *
24990 TCAATCCGCCCCTCTTGATTAGGGGTAAAACATTGGAATGACT
1 TCAATCTG-CCCTCTTGATTAGGGGTAAAAGATTGGAATGACT
25033 GTAGTTTTAA
Statistics
Matches: 144, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
41 64 0.44
42 5 0.03
43 37 0.26
44 36 0.25
45 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (42 bp):
TCAATCTGCCCTCTTGATTAGGGGTAAAAGATTGGAATGACT
Found at i:25019 original size:87 final size:84
Alignment explanation
Indices: 24821--25032 Score: 252
Period size: 87 Copynumber: 2.5 Consensus size: 84
24811 TGGCGTGTCC
* * *
24821 TCAATCTGCCCTTCATGATTAGGGGTAAAAGATTGAAAT--CTTTAATCTGCCTCTCTTGATTAG
1 TCAATCTGCCCTTCTTGATTAGGGGTAAAAGATTGGAATGACTTCAATCTGCCTCTCTTGATTAG
* *
24884 GGGTATAAGATTTGAATCT
66 GGGTAAAAGATTTGAATAT
* * *
24903 TCAATATGTCCTTCTTGATTAGGGATAAAAGATTGGAATGACTTCAATCTGCAC-CTCTTGACTT
1 TCAATCTGCCCTTCTTGATTAGGGGTAAAAGATTGGAATGACTTCAATCTGC-CTCTCTTGA-TT
24967 AGGGGTAAAAGA-TTGAAATGTAT
64 AGGGGTAAAAGATTTG-AA--TAT
* * *
24990 TCAATCCGCCCCTCTTGATTAGGGGTAAAACATTGGAATGACT
1 TCAATCTGCCCTTCTTGATTAGGGGTAAAAGATTGGAATGACT
25033 GTAGTTTTAA
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
82 34 0.31
84 20 0.18
85 16 0.15
87 39 0.36
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (84 bp):
TCAATCTGCCCTTCTTGATTAGGGGTAAAAGATTGGAATGACTTCAATCTGCCTCTCTTGATTAG
GGGTAAAAGATTTGAATAT
Found at i:25386 original size:48 final size:48
Alignment explanation
Indices: 25334--25470 Score: 132
Period size: 50 Copynumber: 2.8 Consensus size: 48
25324 TCGTCGTTGT
* *
25334 GGCCTTAACCTTTCCCATCATATTTCATGGAACCGAATTCGCTATTGC
1 GGCCTTAACCTTTCCCATCACATTTCATGGTACCGAATTCGCTATTGC
* * * * ** * *
25382 GGCCTCAATCC-TCCCCATCACATCTTCTAAGGTACAGGGTTTGCTGTTGC
1 GGCCTTAA-CCTTTCCCATCACAT-TTC-ATGGTACCGAATTCGCTATTGC
**
25432 CTCCTTAACCTTTCCCATCACATTTCATGGTACCGAATT
1 GGCCTTAACCTTTCCCATCACATTTCATGGTACCGAATT
25471 TGTCGTTATG
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
48 26 0.39
49 10 0.15
50 31 0.46
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (48 bp):
GGCCTTAACCTTTCCCATCACATTTCATGGTACCGAATTCGCTATTGC
Found at i:25704 original size:50 final size:50
Alignment explanation
Indices: 25503--25858 Score: 269
Period size: 50 Copynumber: 7.1 Consensus size: 50
25493 CCCATCACAT
* * * * *
25503 CTTT-CTATCACATCTTCTGAGGTA-CAAGGTTCACCGTTACCGCCTCAAT
1 CTTTCCTATCACATCTTCTAAGGTATC-GGGTTCACCGTTGCGGCCTCAAC
* * * * *
25552 CATTCC-ATCACATCTTTTTTTTAAGGTATCGGGTTCACCATAGTGGCCTCAAC
1 CTTTCCTATCACATC----TTCTAAGGTATCGGGTTCACCGTTGCGGCCTCAAC
* * * * * * *
25605 CTTTCCCT-TTATATCTT-TATGGTATCAGGCTCACTGTTGCAGCCTCAAC
1 CTTT-CCTATCACATCTTCTAAGGTATCGGGTTCACCGTTGCGGCCTCAAC
* *
25654 CTTTCCTATCACATCTTCTAAGGTATCGGGTTCGCCGTTGTGGCCTCAAC
1 CTTTCCTATCACATCTTCTAAGGTATCGGGTTCACCGTTGCGGCCTCAAC
* * * *
25704 CTTTCCCATCACAGT-TTCTAAGGTATTGGGTTCACCGTTACGACCTCAAC
1 CTTTCCTATCACA-TCTTCTAAGGTATCGGGTTCACCGTTGCGGCCTCAAC
* * * ** *
25754 CTTTCCCT-TCATATCTTC-ATGGTACCGGGTTCATGGTTGCGACCTCAAC
1 CTTT-CCTATCACATCTTCTAAGGTATCGGGTTCACCGTTGCGGCCTCAAC
* * ** * *
25803 CTTTCCCATCACATCTTCTAAGGTACCGGGTTCGTCGTTACAGCCTCAAC
1 CTTTCCTATCACATCTTCTAAGGTATCGGGTTCACCGTTGCGGCCTCAAC
25853 CTTTCC
1 CTTTCC
25859 CTTTAGATCT
Statistics
Matches: 240, Mismatches: 52, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
48 5 0.02
49 85 0.35
50 112 0.47
51 3 0.01
53 27 0.11
54 8 0.03
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.34
Consensus pattern (50 bp):
CTTTCCTATCACATCTTCTAAGGTATCGGGTTCACCGTTGCGGCCTCAAC
Found at i:25783 original size:99 final size:99
Alignment explanation
Indices: 25598--25912 Score: 323
Period size: 99 Copynumber: 3.2 Consensus size: 99
25588 ACCATAGTGG
* * * * * * * * *
25598 CCTCAACCTTTCCCTTTATATCTT-TATGGTATCAGGCTCACTGTTGCAGCCTCAACCTTT-CCT
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCACCGTTACAGCCTCAACCTTTCCCT
* * * *
25661 ATCACATCTTCTAAGGTATCGGGTTCGCCGTTGTGG
66 -TCACATCTTC-ATGGTACCGGGTTCGCCGTTGCGA
**
25697 CCTCAACCTTTCCCATCACAGT-TTCTAAGGTATTGGGTTCACCGTTAC-GACCTCAACCTTTCC
1 CCTCAACCTTTCCCATCACA-TCTTCTAAGGTACCGGGTTCACCGTTACAG-CCTCAACCTTTCC
* ***
25760 CTTCATATCTTCATGGTACCGGGTTCATGGTTGCGA
64 CTTCACATCTTCATGGTACCGGGTTCGCCGTTGCGA
**
25796 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGTCGTTACAGCCTCAACCTTTCCCT
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCACCGTTACAGCCTCAACCTTTCCCT
* * * * * *
25861 TTAGATCTTTATGGTACCAGGTTTGCCATTGCGA
66 TCACATCTTCATGGTACCGGGTTCGCCGTTGCGA
25895 CCTCAACCTTTCCCATCA
1 CCTCAACCTTTCCCATCA
25913 TGTTTCATGT
Statistics
Matches: 180, Mismatches: 30, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
98 1 0.01
99 137 0.76
100 39 0.22
101 3 0.02
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (99 bp):
CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCACCGTTACAGCCTCAACCTTTCCCT
TCACATCTTCATGGTACCGGGTTCGCCGTTGCGA
Found at i:25859 original size:50 final size:50
Alignment explanation
Indices: 25647--25912 Score: 279
Period size: 50 Copynumber: 5.4 Consensus size: 50
25637 ACTGTTGCAG
* * * *
25647 CCTCAACCTTTCCTATCACATCTTCTAAGGTATCGGGTTCGCCGTTGTGG
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGA
** * *
25697 CCTCAACCTTTCCCATCACAGT-TTCTAAGGTATTGGGTTCACCGTTACGA
1 CCTCAACCTTTCCCATCACA-TCTTCTAAGGTACCGGGTTCGCCGTTGCGA
* * * ***
25747 CCTCAACCTTTCCCTTCATATCTTC-ATGGTACCGGGTTCATGGTTGCGA
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGA
* *
25796 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGTCGTTAC-A
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGA
* * * * * * *
25845 GCCTCAACCTTTCCCTTTAGATCTT-TATGGTACCAGGTTTGCCATTGCGA
1 -CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGA
25895 CCTCAACCTTTCCCATCA
1 CCTCAACCTTTCCCATCA
25913 TGTTTCATGT
Statistics
Matches: 180, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
49 76 0.42
50 103 0.57
51 1 0.01
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (50 bp):
CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGA
Found at i:25902 original size:49 final size:48
Alignment explanation
Indices: 25598--25908 Score: 200
Period size: 50 Copynumber: 6.3 Consensus size: 48
25588 ACCATAGTGG
* * * * * **
25598 CCTCAACCTTTCCCTTTATATCTTTATGGTATCAGGCTCACTGTTGC-A
1 CCTCAACCTTTCCCTTCACATCTTTATGGTACCGGGTTTGC-GTTGCGA
* * * * *
25646 GCCTCAACCTTT-CCTATCACATCTTCTAAGGTATCGGGTTCGCCGTTGTGG
1 -CCTCAACCTTTCCCT-TCACATCTT-TATGGTACCGGGTTTG-CGTTGCGA
* * ** ** *
25697 CCTCAACCTTTCCCATCACAGT-TTCTAAGGTATTGGGTTCACCGTTACGA
1 CCTCAACCTTTCCCTTCACA-TCTT-TATGGTACCGGGTT-TGCGTTGCGA
* *
25747 CCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCATG-GTTGCGA
1 CCTCAACCTTTCCCTTCACATCTTTATGGTACCGGGTT--TGCGTTGCGA
* * * *
25796 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGTCGTTAC-A
1 CCTCAACCTTTCCCTTCACATCTT-TATGGTACCGGGTTTG-CGTTGCGA
* * * *
25845 GCCTCAACCTTTCCCTTTAGATCTTTATGGTACCAGGTTTGCCATTGCGA
1 -CCTCAACCTTTCCCTTCACATCTTTATGGTACCGGGTTTG-CGTTGCGA
25895 CCTCAACCTTTCCC
1 CCTCAACCTTTCCC
25909 ATCATGTTTC
Statistics
Matches: 208, Mismatches: 40, Indels: 28
0.75 0.14 0.10
Matches are distributed among these distances:
48 4 0.02
49 89 0.43
50 111 0.53
51 4 0.02
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (48 bp):
CCTCAACCTTTCCCTTCACATCTTTATGGTACCGGGTTTGCGTTGCGA
Found at i:26927 original size:16 final size:16
Alignment explanation
Indices: 26882--26949 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
26872 AATTTTTCTA
26882 TTTCTTTTTCCTTTTTTCC
1 TTTC-TTTT-CTTTTTT-C
*
26901 TTT-TTTCCTTTTTTC
1 TTTCTTTTCTTTTTTC
26916 TTTCTTTTCTTTCTTT-
1 TTTCTTTTCTTT-TTTC
* *
26932 TTTATTTTATTTTTTC
1 TTTCTTTTCTTTTTTC
26948 TT
1 TT
26950 CATTGAATCC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
15 7 0.17
16 26 0.62
17 6 0.14
19 3 0.07
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTCTTTTTTC
Found at i:26932 original size:9 final size:8
Alignment explanation
Indices: 26886--26915 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
26876 TTTCTATTTC
26886 TTTTTCCT
1 TTTTTCCT
26894 TTTTTCCT
1 TTTTTCCT
26902 TTTTTCCT
1 TTTTTCCT
26910 TTTTTC
1 TTTTTC
26916 TTTCTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCCT
Found at i:26947 original size:28 final size:27
Alignment explanation
Indices: 26874--26949 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
26864 CTATTTCCAA
* *
26874 TTTTTCTATTTCTTTTTCCTTTTTTCCT
1 TTTTTC-ATTTTTTTTTTCTTTTTTCCT
* * *
26902 TTTTTCCTTTTTTCTTTCTTTTCTTTCT
1 TTTTTCATTTTTTTTTTCTTTT-TTCCT
26930 TTTTT-ATTTTATTTTTTCTT
1 TTTTTCATTTT-TTTTTTCTT
26950 CATTGAATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 16 0.41
28 23 0.59
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTTCATTTTTTTTTTCTTTTTTCCT
Found at i:30070 original size:30 final size:30
Alignment explanation
Indices: 30013--30120 Score: 112
Period size: 29 Copynumber: 3.6 Consensus size: 30
30003 TAATTTTCAA
* * *
30013 AAAATTCGGGGGTCAAAATCGAGCTTTTTTG
1 AAAATTC-GGGGTCAAAATCAAACTTTTTGG
* *
30044 AAAATTTGGGGTTAAAATCAAAC-TTTTGG
1 AAAATTCGGGGTCAAAATCAAACTTTTTGG
**
30073 AAAATTCAAGGTCAAAATCAAAC-TTTTGG
1 AAAATTCGGGGTCAAAATCAAACTTTTTGG
*
30102 AAAAGTTCGGGGGCAAAAT
1 AAAA-TTCGGGGTCAAAAT
30121 GTGATTTTTG
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 34 0.53
30 24 0.38
31 6 0.09
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATTCGGGGTCAAAATCAAACTTTTTGG
Found at i:30231 original size:30 final size:29
Alignment explanation
Indices: 30180--30243 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
30170 GAAAAATATC
30180 ATTTTTGAAAGTTTGGGGGTTAAAATGTA
1 ATTTTTGAAAGTTTGGGGGTTAAAATGTA
*
30209 ATTTTTAGAAAAGTTT-GGGGTTAAAATGTG
1 ATTTTT-G-AAAGTTTGGGGGTTAAAATGTA
30239 ATTTT
1 ATTTT
30244 AGGAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 6 0.19
30 19 0.59
31 7 0.22
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (29 bp):
ATTTTTGAAAGTTTGGGGGTTAAAATGTA
Found at i:30260 original size:30 final size:29
Alignment explanation
Indices: 30187--30320 Score: 85
Period size: 30 Copynumber: 4.4 Consensus size: 29
30177 ATCATTTTTG
* *
30187 AAAGTTTGGGGGTTAAAATGTAATTTTTAGA
1 AAAGTTT-AGGGTTAAAATGTGA-TTTTAGA
*
30218 AAAGTTTGGGGTTAAAATGTGATTTTAGGA
1 AAAGTTTAGGGTTAAAATGTGATTTTA-GA
* * *
30248 ATA-TTTAAGGGTTAAATTGTGA-TTTAGGG
1 AAAGTTT-AGGGTTAAAATGTGATTTTA-GA
* **
30277 AAAGTTTAAAGGTCGAAAT-TGGATTTTAGA
1 AAAGTTT-AGGGTTAAAATGT-GATTTTAGA
*
30307 AAGGTTTAAGGGTT
1 AAAGTTT-AGGGTT
30321 TGTTGGAGCC
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
29 17 0.20
30 56 0.67
31 11 0.13
ACGTcount: A:0.34, C:0.01, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAGTTTAGGGTTAAAATGTGATTTTAGA
Found at i:30582 original size:29 final size:28
Alignment explanation
Indices: 30516--30582 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
30506 AATTGAGCTT
* *
30516 TTTGGAAAATTTGGGGTTAAAATCAAAC
1 TTTGGAAAATTTGAGGTCAAAATCAAAC
**
30544 TTTCACAAAATTTGAGGTCAAAATCAAAC
1 TTT-GGAAAATTTGAGGTCAAAATCAAAC
30573 TTCTGGAAAA
1 TT-TGGAAAA
30583 GTTCGAGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.10
29 27 0.87
30 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (28 bp):
TTTGGAAAATTTGAGGTCAAAATCAAAC
Found at i:30790 original size:477 final size:475
Alignment explanation
Indices: 29861--30812 Score: 1478
Period size: 477 Copynumber: 2.0 Consensus size: 475
29851 ACAAATAAAA
29861 AAACATGCAAAACTTAAGCATAAAATTATAAAATACAAAATACGAAAGAATAATAATTACATTTT
1 AAACATGCAAAACTTAAGCATAAAATTATAAAATACAAAATACGAAAGAATAATAATTACATTTT
* * * * *
29926 ATGTACGAAAATTGAAGAAAAAGAAAATAAATCAAACAGGTTCGAAAATTGAGTTTTTGAGAATT
66 ATGTACAAAAATCGAAGAAAAAGAAAATAAATCAAACAGGGTCGAAAATGGAGTTTTCGAGAATT
** * *
29991 CAGGACAAAAAGTAATTTTCAAAAAATTCGGGGGTCAAAATCGAGCTTTTTTGAAAATTTGGGGT
131 CAAAACAAAAAGTAATTTTCAAAAAATTCAGGGGTCAAAATCGAGCTTTTTGGAAAATTTGGGGT
*** * *
30056 TAAAATCAAACTTTTGGAAAATTCAAGGTCAAAATCAAACTTTTGGAAAAGTTCGGGGGCAAAAT
196 TAAAATCAAACTTTCACAAAATTCAAGGTCAAAATCAAACTTCTGGAAAAGTTCGAGGGCAAAAT
* *
30121 GTGATTTTTGGAAGTTTAAGGGCAAATTTGTAATTTTGGAAGATTTGAGGAAAAATATCATTTTT
261 GTGATTTTTGGAAGTTTAAGGGCAAATTTGTAATTTTGGAAGATTCGAGGAAAAATATAATTTTT
** * *
30186 GAAAGTTTGGGGGTTAAAATGTAATTTTTAGAAAAGTTTGGGGTTAAAATGTGATTTTAGGAATA
326 GAAAGTTTGGGGGCCAAAATGTAATTTTTAGAAAAGTTTAGGGTCAAAATGTGATTTTAGGAATA
* * *
30251 TTTAAGGGTTAAATTGTGATTTAGGGAAAGTTTAAAGGTCGAAATTGGATTTTAGAAAGGTTTAA
391 TTTAAGGGTTAAAATGTGATTTAGGGAAAGTTTAAAGGTCAAAATAGGATTTTAGAAAGGTTTAA
*
30316 GGGTTTGTTGGAGCCCAATT
456 GGGTCTGTTGGAGCCCAATT
* *
30336 AAACATGTAAAACTTAAGCATAAAATTAATAAAATATAAAATACGAAAGAATAATAATTACATTT
1 AAACATGCAAAACTTAAGCATAAAATT-ATAAAATACAAAATACGAAAGAATAATAATTACATTT
* *
30401 TATGTACAAAAATCGAAGAAAAAGAAAATAAATCGAACGGGGTCGAAAATGGAG-TTTCGAAGAA
65 TATGTACAAAAATCGAAGAAAAAGAAAATAAATCAAACAGGGTCGAAAATGGAGTTTTCG-AGAA
* ** *
30465 TTCAAAACAAAATTGTAATTTTTGAAAAATTCAGGGGTCAAAATTGAGCTTTTTGGAAAATTTGG
129 TTCAAAACAAAA-AGTAATTTTCAAAAAATTCAGGGGTCAAAATCGAGCTTTTTGGAAAATTTGG
** *
30530 GGTTAAAATCAAACTTTCACAAAATTTGAGGTCAAAATCAAACTTCTGGAAAAGTTCGAGGGTAA
193 GGTTAAAATCAAACTTTCACAAAATTCAAGGTCAAAATCAAACTTCTGGAAAAGTTCGAGGGCAA
*
30595 AATGTGATTTTTGGAAGTTTAAGGGTAAATTTGTAATTTTTGGAAGATTCGAGGAAAAAATATAA
258 AATGTGATTTTTGGAAGTTTAAGGGCAAATTTGTAA-TTTTGGAAGATTCGAGG-AAAAATATAA
*
30660 TTTTTGGAAGTTT-GGGGCCAAAATGTAATTTTTAGAAAAGTTTAGGGTCAAAATGTGATTTTAG
321 TTTTTGAAAGTTTGGGGGCCAAAATGTAATTTTTAGAAAAGTTTAGGGTCAAAATGTGATTTTAG
* * *
30724 GAATA-TTAGGGGTTAAAATGTGATTTAGGGAAAGTTTAAAGGTCAAAATAGGATTTTGGGAAGG
386 GAATATTTAAGGGTTAAAATGTGATTTAGGGAAAGTTTAAAGGTCAAAATAGGATTTTAGAAAGG
30788 TTTAAGGGTCTGTTGGAGCCCAATT
451 TTTAAGGGTCTGTTGGAGCCCAATT
30813 TTGATCAGAC
Statistics
Matches: 432, Mismatches: 40, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
475 30 0.07
476 98 0.23
477 215 0.50
478 68 0.16
479 21 0.05
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (475 bp):
AAACATGCAAAACTTAAGCATAAAATTATAAAATACAAAATACGAAAGAATAATAATTACATTTT
ATGTACAAAAATCGAAGAAAAAGAAAATAAATCAAACAGGGTCGAAAATGGAGTTTTCGAGAATT
CAAAACAAAAAGTAATTTTCAAAAAATTCAGGGGTCAAAATCGAGCTTTTTGGAAAATTTGGGGT
TAAAATCAAACTTTCACAAAATTCAAGGTCAAAATCAAACTTCTGGAAAAGTTCGAGGGCAAAAT
GTGATTTTTGGAAGTTTAAGGGCAAATTTGTAATTTTGGAAGATTCGAGGAAAAATATAATTTTT
GAAAGTTTGGGGGCCAAAATGTAATTTTTAGAAAAGTTTAGGGTCAAAATGTGATTTTAGGAATA
TTTAAGGGTTAAAATGTGATTTAGGGAAAGTTTAAAGGTCAAAATAGGATTTTAGAAAGGTTTAA
GGGTCTGTTGGAGCCCAATT
Found at i:30878 original size:6 final size:7
Alignment explanation
Indices: 30847--30876 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
30837 AAATGGGACC
30847 AAATTTT
1 AAATTTT
*
30854 AATTTTT
1 AAATTTT
30861 AAATTTT
1 AAATTTT
30868 AAATTTT
1 AAATTTT
30875 AA
1 AA
30877 TTTATTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:30901 original size:17 final size:17
Alignment explanation
Indices: 30863--30939 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
30853 TAATTTTTAA
*
30863 ATTTTAAATTTTAATTT
1 ATTTTAAATTTGAATTT
*
30880 A-TTTAAGTTTGAATTT
1 ATTTTAAATTTGAATTT
*
30896 ATTTTAAATTTGAACTT
1 ATTTTAAATTTGAATTT
* * *
30913 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTGAATTT
30930 ATTTTAAATT
1 ATTTTAAATT
30940 AAATTTAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
16 14 0.29
17 35 0.71
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTGAATTT
Found at i:30901 original size:33 final size:34
Alignment explanation
Indices: 30863--30939 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
30853 TAATTTTTAA
* * *
30863 ATTTTAAATTTTAATTTA-TTTAAGTTTGAATTT
1 ATTTTAAATTTGAACTTATTTTAAGTTTAAATTT
*
30896 ATTTTAAATTTGAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTGAACTTATTTTAAGTTTAAATTT
30930 ATTTTAAATT
1 ATTTTAAATT
30940 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 16 0.41
34 23 0.59
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.58
Consensus pattern (34 bp):
ATTTTAAATTTGAACTTATTTTAAGTTTAAATTT
Found at i:32738 original size:30 final size:29
Alignment explanation
Indices: 32721--33191 Score: 395
Period size: 29 Copynumber: 16.2 Consensus size: 29
32711 TCTAATAATC
* *
32721 ACATTTTAACCCTTAAACTTTTCC-AAAATA
1 ACATTTTTACCCTTAAAC--TTCCAAAAATT
* * *
32751 ACATTTTGACCCTTAAATTTTTCC-AAAACT
1 ACATTTTTACCCTTAAA--CTTCCAAAAATT
* * ** * *
32781 ATATTTTAACCCCGAACATTTCC-AAAGTT
1 ACATTTTTACCCTTAA-ACTTCCAAAAATT
* *
32810 ACATTTTGACCCTAAAACTTCTC-AAAATT
1 ACATTTTTACCCTTAAACTTC-CAAAAATT
*
32839 ACACTTTT-CCCTTAAACTTCCAAAAATT
1 ACATTTTTACCCTTAAACTTCCAAAAATT
*
32867 ACA-TTTTACCCCTAAACTTCCAAAAATT
1 ACATTTTTACCCTTAAACTTCCAAAAATT
*
32895 ACATTTTTACCC-TAGAACTTCCAAAAATC
1 ACATTTTTACCCTTA-AACTTCCAAAAATT
** *
32924 ACATTTTTACCCTCGAACTTCCAAAAATC
1 ACATTTTTACCCTTAAACTTCCAAAAATT
* *
32953 ACATTTTTGCCCTCAAACTTCCAAAAATT
1 ACATTTTTACCCTTAAACTTCCAAAAATT
* *
32982 ACATTTTTTCCCTTAAACTTCTAAAAATT
1 ACATTTTTACCCTTAAACTTCCAAAAATT
* ** * *
33011 ATATTTTTTACCCTCGAACTTCTAAAAATC
1 ACA-TTTTTACCCTTAAACTTCCAAAAATT
* * * * *
33041 ATATATTTACCCTTGATCTTCTAAAAATT
1 ACATTTTTACCCTTAAACTTCCAAAAATT
* *
33070 ACATTTTTTCCCTTAAACTTCCAAAAATC
1 ACATTTTTACCCTTAAACTTCCAAAAATT
*
33099 ACATTTTTACCC-TAGACTTCTCAAAAATT
1 ACATTTTTACCCTTAAACTTC-CAAAAATT
* * * *
33128 ATATTTTTACCC-CAAACTCTCCCAAAATG
1 ACATTTTTACCCTTAAACT-TCCAAAAATT
*
33157 ACATTTTTGCCCTTAAAACTTTCC-AAAATT
1 ACATTTTTACCCTT-AAAC-TTCCAAAAATT
33187 ACATT
1 ACATT
33192 CTAACCCAAA
Statistics
Matches: 369, Mismatches: 57, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
27 5 0.01
28 55 0.15
29 227 0.62
30 73 0.20
31 8 0.02
32 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
ACATTTTTACCCTTAAACTTCCAAAAATT
Found at i:33638 original size:97 final size:97
Alignment explanation
Indices: 33472--33654 Score: 321
Period size: 97 Copynumber: 1.9 Consensus size: 97
33462 AAAATATTTA
* * *
33472 AAATCGAGGCAATATTCCTTTATTTTGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGTGAT
1 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
33537 TTTTCTTCAAACCGGGATAATTGAATACCCTT
66 TTTTCTTCAAACCGGGATAATTGAATACCCTT
* *
33569 AAATCGAGGCAATATTCTTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGTGCGAT
1 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
33634 TTTTCTTCAAACCGGGATAAT
66 TTTTCTTCAAACCGGGATAAT
33655 CAAATATCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 81 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
TTTTCTTCAAACCGGGATAATTGAATACCCTT
Found at i:45297 original size:39 final size:39
Alignment explanation
Indices: 45210--45653 Score: 203
Period size: 39 Copynumber: 11.3 Consensus size: 39
45200 CAAGATTCCG
*
45210 ATCTCTTACCCCAAG-TCTGGGGCAGATCA-CAGTCA-TCA
1 ATCTCTTACCCCGAGCT-TGGGGCAGATCACCA-TCAGTCA
*
45248 GATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGTCA
1 -ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCA
** * * ** * * *
45288 ATCTCTTACCCTAATCTTGGGGTAGA-CTGCAGCCGTTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG-TCA
* * *
45327 ATCTCTTACCTCGAGCCTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCA
* *
45366 TTTGATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAGCCA
1 ----ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCA
* * * * * * *
45409 ATCTCTTATCCCGATCATGGGGCATATTGTAGC-T-A-TCTG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CACCATCAGTC-A
* * * * * **
45448 ATTTCTTACCTCGAGCCTAGGGCAGATAATTATCAG-CAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC-A
* * * *
45487 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCAT---TCG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGTCA
* * *
45526 ATCTTTTACCCCGAGCTTGGGACAGATCATCATCAG-CAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC-A
* * *** * *
45565 ATCTCTTACCCCGAGCCTAGGGCAGAT-TGTAGTCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGTCA
* * * *
45604 ATCTTTTACCGCGAGCCTGGGGGCAGATCATCATCAGTCA
1 ATCTCTTACCCCGAG-CTTGGGGCAGATCACCATCAGTCA
45644 ATCTCTTACC
1 ATCTCTTACC
45654 TCGATCATGG
Statistics
Matches: 297, Mismatches: 81, Indels: 53
0.69 0.19 0.12
Matches are distributed among these distances:
36 3 0.01
37 2 0.01
38 11 0.04
39 200 0.67
40 39 0.13
41 4 0.01
42 2 0.01
43 36 0.12
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCA
Found at i:45430 original size:121 final size:116
Alignment explanation
Indices: 45208--45474 Score: 297
Period size: 121 Copynumber: 2.2 Consensus size: 116
45198 TTCAAGATTC
* * * * * *
45208 CGATCTCTTACCCCAAGTCTGGGGCAGATCACAGTCATCAGATCTTTTACCCCGAGCTTGGGGCA
1 CGATCTCTTACCTCGAGCCTGGGGCAGATCACAGTCACCAGATCTCTTACCCCAAGCTTGGGGCA
* * *
45273 GATCACCATCAGTCAATCTCTTACCCTAATCTTGGGGTAGACTGCAGCCGT-T
66 GATCACCATCAGCCAATCTCTTACCCTAATCATGGGGCAGACTGCAG-C-TAT
45325 CGATCTCTTACCTCGAGCCTGGGGCAGATCACCA-TCAGCCATTTGATCTCTTACCCCAAGCTTG
1 CGATCTCTTACCTCGAGCCTGGGGCAGATCA-CAGTCA-CCA---GATCTCTTACCCCAAGCTTG
* * * *
45389 GGGCAGATCACCATCAGCCAATCTCTTATCCC-GATCATGGGGCATATTGTAGCTAT
61 GGGCAGATCACCATCAGCCAATCTCTTA-CCCTAATCATGGGGCAGACTGCAGCTAT
* *
45445 CTGATTTCTTACCTCGAGCCTAGGGCAGAT
1 C-GATCTCTTACCTCGAGCCTGGGGCAGAT
45475 AATTATCAGC
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
117 31 0.24
118 4 0.03
119 1 0.01
120 3 0.02
121 85 0.67
122 3 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (116 bp):
CGATCTCTTACCTCGAGCCTGGGGCAGATCACAGTCACCAGATCTCTTACCCCAAGCTTGGGGCA
GATCACCATCAGCCAATCTCTTACCCTAATCATGGGGCAGACTGCAGCTAT
Found at i:45474 original size:78 final size:78
Alignment explanation
Indices: 45369--45672 Score: 312
Period size: 78 Copynumber: 3.9 Consensus size: 78
45359 TCAGCCATTT
* * * * * * * * * *
45369 GATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAGCCAATCTCTTATCCCGATCATGGGGCAT
1 GATCTTTTACCCCGAGCCTAGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCATAGGGCAG
45434 ATTGTAGCTA-TC
66 ATTGTAGCTATTC
* * * *
45446 TGAT-TTCTTACCTCGAGCCTAGGGCAGATAATTATCAGCAAATCTCTTACCCCGAGCCTAGGGC
1 -GATCTT-TTACCCCGAGCCTAGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCATAGGGC
*
45510 AGATTGTAGCCATTC
64 AGATTGTAGCTATTC
* *
45525 GATCTTTTACCCCGAG-CTTGGGACAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
1 GATCTTTTACCCCGAGCCTAGGG-CAGATCATCATCAGCAAATCTCTTACCCCGAGCATAGGGCA
45589 GATTGTAG-TCATTC
65 GATTGTAGCT-ATTC
* * * * * *
45603 GATCTTTTACCGCGAGCCTGGGGGCAGATCATCATCAGTC-AATCTCTTACCTCGATCATGGGGT
1 GATCTTTTACCCCGAGCCT-AGGGCAGATCATCATCAG-CAAATCTCTTACCCCGAGCATAGGGC
45667 AGATTG
64 AGATTG
45673 CAGTCATTCG
Statistics
Matches: 191, Mismatches: 27, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
77 6 0.03
78 136 0.71
79 45 0.24
80 4 0.02
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (78 bp):
GATCTTTTACCCCGAGCCTAGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCATAGGGCAG
ATTGTAGCTATTC
Found at i:45484 original size:121 final size:121
Alignment explanation
Indices: 45248--45476 Score: 302
Period size: 121 Copynumber: 1.9 Consensus size: 121
45238 ACAGTCATCA
* * * * *
45248 GATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCTAATCTTGGGGTAG
1 GATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCTAATCATGGGGCAG
* *
45313 ACTGCAGCCGTTCGATCTCTTACCTCGAGCCTGGGGCAGATCACCATCAGCCATTT
66 ACTGCAGCCGTTCGATCTCTTACCTCGAGCCTAGGGCAGATAACCATCAGCCATTT
*
45369 GATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAGCCAATCTCTTATCCC-GATCATGGGGCA
1 GATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAGCCAATCTCTTA-CCCTAATCATGGGGCA
* * * *
45433 TATTGTAG-C-TATCTGATTTCTTACCTCGAGCCTAGGGCAGATAA
65 GACTGCAGCCGT-TC-GATCTCTTACCTCGAGCCTAGGGCAGATAA
45477 TTATCAGCAA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
119 1 0.01
120 3 0.03
121 86 0.92
122 3 0.03
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (121 bp):
GATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCTAATCATGGGGCAG
ACTGCAGCCGTTCGATCTCTTACCTCGAGCCTAGGGCAGATAACCATCAGCCATTT
Found at i:46052 original size:7 final size:7
Alignment explanation
Indices: 46040--46069 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
46030 TGAGACCCAA
46040 TTTTAAT
1 TTTTAAT
46047 TTTTAAT
1 TTTTAAT
46054 TTTTAAT
1 TTTTAAT
46061 TTTTAAT
1 TTTTAAT
46068 TT
1 TT
46070 ATTTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:46096 original size:34 final size:35
Alignment explanation
Indices: 46052--46129 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 35
46042 TTAATTTTTA
* * * *
46052 ATTTTTAATTTTTAATTTATTTT-AGTTTGAATTT
1 ATTTTAAATTTTGAACTTATTTTGAGTTTAAATTT
46086 ATTTTAAA-TTTGAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTTGAACTTATTTTGAGTTTAAATTT
46120 ATTTTAAATT
1 ATTTTAAATT
46130 AAATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 12 0.32
34 25 0.66
35 1 0.03
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (35 bp):
ATTTTAAATTTTGAACTTATTTTGAGTTTAAATTT
Found at i:46099 original size:17 final size:17
Alignment explanation
Indices: 46054--46129 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 17
46044 AATTTTTAAT
* *
46054 TTTTAATTTTTAATTTA
1 TTTTAAATTTGAATTTA
*
46071 TTTT-AGTTTGAATTTA
1 TTTTAAATTTGAATTTA
*
46087 TTTTAAATTTGAACTTA
1 TTTTAAATTTGAATTTA
* * *
46104 TTTTGAGTTTAAATTTA
1 TTTTAAATTTGAATTTA
46121 TTTTAAATT
1 TTTTAAATT
46130 AAATTTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
16 14 0.29
17 34 0.71
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTGAATTTA
Found at i:46820 original size:10 final size:11
Alignment explanation
Indices: 46805--46834 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
46795 TAATAAACAC
46805 ATTAAATAA-T
1 ATTAAATAATT
46815 ATTAAATAATT
1 ATTAAATAATT
46826 ATTAAATAA
1 ATTAAATAA
46835 AAAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAATAATT
Found at i:46983 original size:3 final size:3
Alignment explanation
Indices: 46975--47021 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
46965 CATACATGAA
* * * *
46975 AAT AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT ATT AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
47022 AAGGGCAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:47970 original size:29 final size:29
Alignment explanation
Indices: 47923--48189 Score: 92
Period size: 29 Copynumber: 9.2 Consensus size: 29
47913 CCCAAAAGGT
*
47923 CCCTAAACTTTT-TAGAAATCACA-TTTAA
1 CCCTAAACTTTTCCA-AAATCACATTTTAA
*
47951 CCCCTAAACTTTTCCAAAATTACATTTTAA
1 -CCCTAAACTTTTCCAAAATCACATTTTAA
* * *
47981 -CCTAAAATTTTTCCAAAA-CTATATTTTGA
1 CCCT-AAACTTTTCCAAAATC-ACATTTTAA
* * * *
48010 CCCTCGAACATTTCCAAAATTACATTTTGA
1 CCCT-AAACTTTTCCAAAATCACATTTTAA
* * *
48040 -CCTCAAACTTCT-CAAAATTACACTTTT-T
1 CCCT-AAACTTTTCCAAAATCACA-TTTTAA
** * **
48068 CCCTCGA-TCTTCCAATAATCACATTTTGG
1 CCCTAAACTTTTCCAA-AATCACATTTTAA
* * * * *
48097 CTCC-GAACTTCTCAAAAATCATATTTTTA
1 C-CCTAAACTTTTCCAAAATCACATTTTAA
* * * *
48126 -CCTCGAAC--TCCCAAAATGACATTTTTAT
1 CCCT-AAACTTTTCCAAAATCACA-TTTTAA
*
48154 CCCTAAAAC-TTTCCAAAATTACATTTTAA
1 CCCT-AAACTTTTCCAAAATCACATTTTAA
48183 CCCTAAA
1 CCCTAAA
48190 TTCTTCGAAA
Statistics
Matches: 178, Mismatches: 42, Indels: 37
0.69 0.16 0.14
Matches are distributed among these distances:
27 12 0.07
28 28 0.16
29 92 0.52
30 46 0.26
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATCACATTTTAA
Found at i:47982 original size:30 final size:29
Alignment explanation
Indices: 47923--48066 Score: 109
Period size: 29 Copynumber: 4.9 Consensus size: 29
47913 CCCAAAAGGT
* *
47923 CCCTAAACTTTT-TAGAAATCACA-TTTAA
1 CCCTAAACTTTTCCA-AAATTACATTTTAA
47951 CCCCTAAACTTTTCCAAAATTACATTTTAA
1 -CCCTAAACTTTTCCAAAATTACATTTTAA
* * * *
47981 -CCTAAAATTTTTCCAAAACTATATTTTGA
1 CCCT-AAACTTTTCCAAAATTACATTTTAA
* * *
48010 CCCTCGAACATTTCCAAAATTACATTTTGA
1 CCCT-AAACTTTTCCAAAATTACATTTTAA
*
48040 -CCTCAAACTTCT-CAAAATTACACTTTT
1 CCCT-AAACTTTTCCAAAATTACA-TTTT
48067 TCCCTCGATC
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
28 13 0.14
29 53 0.56
30 29 0.31
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:48948 original size:42 final size:42
Alignment explanation
Indices: 48892--48975 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
48882 AATTTTAATT
48892 TTTTTTGAGAGAATGGACCTGGGCTAGTATTTCTCATTATAA
1 TTTTTTGAGAGAATGGACCTGGGCTAGTATTTCTCATTATAA
48934 TTTTTTGAGAGAATGGACCTGGGCTAGTATTTCTCATTATAA
1 TTTTTTGAGAGAATGGACCTGGGCTAGTATTTCTCATTATAA
48976 ATGAAATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (42 bp):
TTTTTTGAGAGAATGGACCTGGGCTAGTATTTCTCATTATAA
Found at i:49280 original size:21 final size:22
Alignment explanation
Indices: 49256--49306 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
49246 ATGTGTCACA
49256 AAATGAAA-TTAAAATG-AAACC
1 AAATGAAAGTT-AAATGAAAACC
49277 AAATGAAAGTTAAATGAAAACC
1 AAATGAAAGTTAAATGAAAACC
*
49299 TAATGAAA
1 AAATGAAA
49307 AAAGCAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.20
Consensus pattern (22 bp):
AAATGAAAGTTAAATGAAAACC
Found at i:51437 original size:11 final size:11
Alignment explanation
Indices: 51421--51445 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
51411 TTCTTTTGCT
51421 TTTATTATTTA
1 TTTATTATTTA
51432 TTTATTATTTA
1 TTTATTATTTA
51443 TTT
1 TTT
51446 CTATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:51947 original size:18 final size:18
Alignment explanation
Indices: 51926--51967 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
51916 TTGGATTTGT
51926 AATTTAAATTTAAAA-TAA
1 AATTTAAA-TTAAAACTAA
51944 AATTTAAATTAAAACCTAA
1 AATTTAAATTAAAA-CTAA
51963 AATTT
1 AATTT
51968 GGTTTACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 8 0.36
19 8 0.36
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTAAATTAAAACTAA
Found at i:56256 original size:15 final size:16
Alignment explanation
Indices: 56231--56262 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
56221 TGGAAAAAAA
56231 CAAATAACAAATAACT
1 CAAATAACAAATAACT
56247 CAAA-AACAAATAACT
1 CAAATAACAAATAACT
56262 C
1 C
56263 TTAAAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (16 bp):
CAAATAACAAATAACT
Found at i:56422 original size:24 final size:24
Alignment explanation
Indices: 56371--56422 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
56361 TTTGTAGGTC
* *
56371 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
56395 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
56419 AAAT
1 AAAT
56423 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:57160 original size:24 final size:24
Alignment explanation
Indices: 57133--57180 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
57123 TAGGAATATG
*
57133 AAAGGTTAAAGA-AGATGGAAGGTT
1 AAAGG-TAAAGAGAGATGAAAGGTT
*
57157 AAAGGTCAAGAGAGATGAAAGGTT
1 AAAGGTAAAGAGAGATGAAAGGTT
57181 GAACATCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.19
Consensus pattern (24 bp):
AAAGGTAAAGAGAGATGAAAGGTT
Found at i:62531 original size:17 final size:17
Alignment explanation
Indices: 62504--62545 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
62494 GGAAAAAGTA
62504 GTTACAAGAATATGAAAG
1 GTTA-AAGAATATGAAAG
*
62522 GTTAAAGAATATGGAAG
1 GTTAAAGAATATGAAAG
62539 GTTAAAG
1 GTTAAAG
62546 GTCAAGGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (17 bp):
GTTAAAGAATATGAAAG
Found at i:62658 original size:18 final size:19
Alignment explanation
Indices: 62635--62670 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
62625 AAAATTTTAA
62635 AATTTTAAAAA-TATTTTG
1 AATTTTAAAAATTATTTTG
62653 AATTTTAAAAATTATTTT
1 AATTTTAAAAATTATTTT
62671 TGATTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:64288 original size:24 final size:24
Alignment explanation
Indices: 64252--64317 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
64242 GTGGAACCAG
64252 TAGAAAATGAAGATCCAACTCCAA
1 TAGAAAATGAAGATCCAACTCCAA
* * *
64276 TAGAAAATAAAGATCCAACTCTAG
1 TAGAAAATGAAGATCCAACTCCAA
64300 TAGAAAATGAAGATCCAA
1 TAGAAAATGAAGATCCAA
64318 ATCCGTGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.18
Consensus pattern (24 bp):
TAGAAAATGAAGATCCAACTCCAA
Found at i:67078 original size:14 final size:14
Alignment explanation
Indices: 67055--67132 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
67045 TTTAAGCCTT
*
67055 AAACCCTAAATATG
1 AAACCATAAATATG
67069 AAACCATAAATCAT-
1 AAACCATAAAT-ATG
* **
67083 AAACCCTAAACGTG
1 AAACCATAAATATG
* *
67097 AAACCTTAAATATT
1 AAACCATAAATATG
*
67111 AAA-CACTAAACATG
1 AAACCA-TAAATATG
67125 AAACCATA
1 AAACCATA
67133 TGTGAAATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
13 2 0.04
14 43 0.88
15 4 0.08
ACGTcount: A:0.53, C:0.22, G:0.05, T:0.21
Consensus pattern (14 bp):
AAACCATAAATATG
Found at i:67098 original size:28 final size:28
Alignment explanation
Indices: 67053--67132 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
67043 ATTTTAAGCC
*
67053 TTAAACCCTAAATATGAAACCATAAATCA
1 TTAAACCCTAAACATGAAACCATAAAT-A
* *
67082 -TAAACCCTAAACGTGAAACCTTAAATA
1 TTAAACCCTAAACATGAAACCATAAATA
*
67109 TTAAACACTAAACATGAAACCATA
1 TTAAACCCTAAACATGAAACCATA
67133 TGTGAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (28 bp):
TTAAACCCTAAACATGAAACCATAAATA
Found at i:68081 original size:43 final size:43
Alignment explanation
Indices: 68018--68114 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
68008 AACTACACAA
* * **
68018 TTAATAACATGTCACGATATTAACAAGAGTCGGGTAATATAAT
1 TTAATAACATGCCACAATATTAACAAGAGTCAAGTAATATAAT
*
68061 TTAATAACATGCCACAATATTAACATGAGTCAAGTAATATAAT
1 TTAATAACATGCCACAATATTAACAAGAGTCAAGTAATATAAT
68104 TTAATAACATG
1 TTAATAACATG
68115 TCGATGAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (43 bp):
TTAATAACATGCCACAATATTAACAAGAGTCAAGTAATATAAT
Found at i:69470 original size:20 final size:21
Alignment explanation
Indices: 69445--69488 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
69435 AATATTCCTT
69445 AATTAC-TACTAACAAAATAA
1 AATTACTTACTAACAAAATAA
69465 AATTACTTACTAACAAAATAA
1 AATTACTTACTAACAAAATAA
69486 AAT
1 AAT
69489 AGAATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTACTTACTAACAAAATAA
Found at i:69587 original size:23 final size:25
Alignment explanation
Indices: 69561--69610 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
69551 ACTATATAAA
*
69561 AAAAATTAAA-TAA-CAAATCAAAT
1 AAAAATTAAATTAAGCAAAACAAAT
69584 AAAAATTAAATTAAGCAAAACAAAT
1 AAAAATTAAATTAAGCAAAACAAAT
69609 AA
1 AA
69611 CTTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 10 0.42
24 3 0.12
25 11 0.46
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.20
Consensus pattern (25 bp):
AAAAATTAAATTAAGCAAAACAAAT
Found at i:69660 original size:28 final size:27
Alignment explanation
Indices: 69600--69661 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 27
69590 TAAATTAAGC
*
69600 AAAAC-AAATAACTTAAAATAATAATT
1 AAAACAAAATAACTTAAAATAACAATT
69626 ACTAAACAAATATAACTTTAAAATAACAA-T
1 A--AAACAAA-ATAAC-TTAAAATAACAATT
69656 AAAACA
1 AAAACA
69662 TTTACATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
26 1 0.03
28 9 0.30
29 2 0.07
30 7 0.23
31 11 0.37
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAACAAAATAACTTAAAATAACAATT
Found at i:69891 original size:4 final size:4
Alignment explanation
Indices: 69882--69949 Score: 73
Period size: 4 Copynumber: 16.5 Consensus size: 4
69872 CATTATTCTG
* * * * *
69882 TTTC TTTC TTTC TTTTC TCTC CTTG TTTC TTTC TTTT TTTC TTTT TCTTC
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC
69932 TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TT
69950 GTTCTTCTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
4 45 0.87
5 7 0.13
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:69914 original size:25 final size:26
Alignment explanation
Indices: 69880--69946 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 26
69870 AACATTATTC
69880 TGTTTCTTTCTTTCTTTTC-TCTCCT
1 TGTTTCTTTCTTTCTTTTCTTCTCCT
* *
69905 TGTTTCTTTCTTT-TTTTCTTTTTCT
1 TGTTTCTTTCTTTCTTTTCTTCTCCT
*
69930 TCTTTCTTTCTTTCTTT
1 TGTTTCTTTCTTTCTTT
69947 CTTGTTCTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.14
25 29 0.78
26 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (26 bp):
TGTTTCTTTCTTTCTTTTCTTCTCCT
Found at i:69932 original size:21 final size:21
Alignment explanation
Indices: 69877--69955 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
69867 AATAACATTA
*
69877 TTCTGTTTCTTTCTTTCTTTTCT
1 TTCTTTTTC-TTCTTTCTTTT-T
* * *
69900 CTCCTTGT-TTCTTTCTTTTT
1 TTCTTTTTCTTCTTTCTTTTT
*
69920 TTCTTTTTCTTCTTTCTTTCT
1 TTCTTTTTCTTCTTTCTTTTT
*
69941 TTCTTTCTTGTTCTT
1 TTCTTT-TTCTTCTT
69956 CTCTCTCGTC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
20 6 0.13
21 28 0.62
22 7 0.16
23 4 0.09
ACGTcount: A:0.00, C:0.23, G:0.04, T:0.73
Consensus pattern (21 bp):
TTCTTTTTCTTCTTTCTTTTT
Found at i:69947 original size:25 final size:25
Alignment explanation
Indices: 69882--69957 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
69872 CATTATTCTG
* *
69882 TTTCTTTCTTTCTTT-TCTCTCCTTG
1 TTTCTTTCTTTCTTTCT-TCTTCTTC
* *
69907 TTTCTTTCTTTTTTTCTTTTTCTTC
1 TTTCTTTCTTTCTTTCTTCTTCTTC
*
69932 TTTCTTTCTTTCTTTCTTGTTCTTC
1 TTTCTTTCTTTCTTTCTTCTTCTTC
69957 T
1 T
69958 CTCTCGTCGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
25 43 0.98
26 1 0.02
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (25 bp):
TTTCTTTCTTTCTTTCTTCTTCTTC
Found at i:69957 original size:21 final size:19
Alignment explanation
Indices: 69886--69941 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
69876 ATTCTGTTTC
*
69886 TTTCTTTCTTTTCTCTCCTTG
1 TTTCTTTC-TTTCT-TTCTTG
*
69907 TTTCTTTCTTTTTTTCTT-
1 TTTCTTTCTTTCTTTCTTG
69925 TTTC-TTCTTTCTTTCTT
1 TTTCTTTCTTTCTTTCTT
69942 TCTTTCTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 12 0.38
18 4 0.12
19 4 0.12
20 4 0.12
21 8 0.25
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTCTTTCTTTCTTTCTTG
Found at i:71223 original size:59 final size:59
Alignment explanation
Indices: 71147--71270 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 59
71137 TGATACTTAA
* * * ** * *
71147 ATTTTTTTATCCAATTTGGTACCTGAATTTGGTATTTTTTCCAAATTTGGTATCTAAAC
1 ATTTTTTTACCCAATTTGGTACCTAAACTTGACATTTTTTCCAAATTTAGTACCTAAAC
*
71206 ATTTTTTTACCCAATTTGGTACCTAAACTTGACATTTTTTCCTAATTTAGTACCTAAAC
1 ATTTTTTTACCCAATTTGGTACCTAAACTTGACATTTTTTCCAAATTTAGTACCTAAAC
71265 -TTTTTT
1 ATTTTTT
71271 AAGATTCAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 6 0.11
59 51 0.89
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (59 bp):
ATTTTTTTACCCAATTTGGTACCTAAACTTGACATTTTTTCCAAATTTAGTACCTAAAC
Found at i:71253 original size:31 final size:28
Alignment explanation
Indices: 71150--71266 Score: 94
Period size: 31 Copynumber: 3.9 Consensus size: 28
71140 TACTTAAATT
* *
71150 TTTTTATCCAATTTGGTACCTGAATTTGGTA
1 TTTTT-TCCAATTTGGTACCTAAACTT-G-A
*
71181 TTTTTTCCAAATTTGGTATCTAAACATT--
1 TTTTTTCC-AATTTGGTACCTAAAC-TTGA
*
71209 TTTTTACCCAATTTGGTACCTAAACTTGACA
1 TTTTT-TCCAATTTGGTACCTAAACTTG--A
*
71240 TTTTTTCCTAATTTAGTACCTAAACTT
1 TTTTTTCC-AATTTGGTACCTAAACTT
71267 TTTTAAGATT
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
27 2 0.03
28 20 0.28
29 2 0.03
30 5 0.07
31 40 0.56
32 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (28 bp):
TTTTTTCCAATTTGGTACCTAAACTTGA
Found at i:71563 original size:29 final size:29
Alignment explanation
Indices: 71490--71564 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
71480 GGACCCCAAA
* *
71490 AAATTTAGATACCAACTTAAAAAATTGTC
1 AAATTTAGATACCAAATTAAAAAATTATC
* *
71519 AAATTTAAATAACAAATTAAAATAA-TATC
1 AAATTTAGATACCAAATTAAAA-AATTATC
*
71548 AAATTCAGATACCAAAT
1 AAATTTAGATACCAAAT
71565 ATTATATTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 36 0.95
30 2 0.05
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (29 bp):
AAATTTAGATACCAAATTAAAAAATTATC
Found at i:72503 original size:24 final size:24
Alignment explanation
Indices: 72476--72526 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
72466 TTTTAAGAAA
*
72476 TTTAA-TTTTTTTCTTTTATGTTCT
1 TTTAACTTTTTTT-TTTCATGTTCT
*
72500 TTTAACTTTTTTTTTTCATTTTCT
1 TTTAACTTTTTTTTTTCATGTTCT
72524 TTT
1 TTT
72527 GCTTCTCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTAACTTTTTTTTTTCATGTTCT
Found at i:72967 original size:15 final size:15
Alignment explanation
Indices: 72947--72978 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
72937 ACAACACAAT
72947 AACATAAATAATTAA
1 AACATAAATAATTAA
*
72962 AACATAAATGATTAA
1 AACATAAATAATTAA
72977 AA
1 AA
72979 AAAAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (15 bp):
AACATAAATAATTAA
Found at i:73131 original size:33 final size:33
Alignment explanation
Indices: 73094--73159 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
73084 CTTATTTTTT
*
73094 TAATT-ATTTTTTAATAATATATTTTAATTATTG
1 TAATTAATTTTTTAATAAT-TATTTAAATTATTG
* *
73127 TAATTCAATTTTTTATTTATTATTTAAATTATT
1 TAATT-AATTTTTTAATAATTATTTAAATTATT
73160 AAATATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 5 0.18
34 12 0.43
35 11 0.39
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (33 bp):
TAATTAATTTTTTAATAATTATTTAAATTATTG
Found at i:78989 original size:41 final size:41
Alignment explanation
Indices: 78931--79178 Score: 316
Period size: 41 Copynumber: 6.0 Consensus size: 41
78921 AATGTCATAA
* * *
78931 AAGCGCCGCTAATGGTCAGGGCATTAGTGGTGCTTTCTCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCTCAT
* * *
78972 AAGCGCCACTAAAGGTCAGGGCACTAGCGACGCTTTCTCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCTCAT
* * * *
79013 AAGTGCCGTTAAAGGTCAGGGCATTAGCGGTGCTTTCACAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCTCAT
* * * *
79054 AAGCGCCGCTAAAAGTCAAGGCATTAGCGACGCTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCTCAT
* * *
79095 AGGCACCGCTAAAGGTCAGGGTATTAGCGGCGCTTTCTCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCTCAT
* * *
79136 AAGCGACGCTAAAGGTCACGGTATTAGCGGCGCTTTCTCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCTCAT
79177 AA
1 AA
79179 ACGATCCAGC
Statistics
Matches: 176, Mismatches: 31, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 176 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.24
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCTCAT
Found at i:85941 original size:43 final size:43
Alignment explanation
Indices: 85893--86153 Score: 269
Period size: 42 Copynumber: 6.1 Consensus size: 43
85883 TAATTTAGTG
* **
85893 GCGTTTGTGAGAAAAGCGCCGCTAAAGACTGTGTTCTTTAGCA
1 GCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* *
85936 CCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
1 GCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* ** **
85979 GCATTTGTG-GAGAAAGCGCCGCTAAAGAAAATG-TCTTTAGTG
1 GCGTTTGTGAG-GAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* * * *
86021 GCATTTGTGGGGAAAGCGCCGTTAAAGACCATGTTCTTTAGCG
1 GCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* * * * *
86064 GCGTTTGT-AGGAAAGCGCCGTTAAAGAACATGGTCTTTAACG
1 GCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* * * * *
86106 GGGATTGTG-GGTAAGCGCCGCTAAAGACCATGTTCTATAGTA
1 GCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
86148 GCGTTT
1 GCGTTT
86154 TTTCACATAA
Statistics
Matches: 182, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
42 101 0.55
43 81 0.45
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
GCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
Found at i:86152 original size:84 final size:85
Alignment explanation
Indices: 85893--86153 Score: 289
Period size: 85 Copynumber: 3.1 Consensus size: 85
85883 TAATTTAGTG
*** *** *
85893 GCGTTTGT-GAGAAAAGCGCCGCTAAAGACTGTGTTCTTTAGCACCGTTTGTGGGGAAAGCGCCG
1 GCGTTTGTAGAG-AAAGCGCCGCTAAAGAAAATG-TCTTTAGTGGCATTTGTGGGGAAAGCGCCG
85957 CTAAAGACCATGTTCTTTAGCA
64 CTAAAGACCATGTTCTTTAGCA
* * *
85979 GCATTTGTGGAGAAAGCGCCGCTAAAGAAAATGTCTTTAGTGGCATTTGTGGGGAAAGCGCCGTT
1 GCGTTTGTAGAGAAAGCGCCGCTAAAGAAAATGTCTTTAGTGGCATTTGTGGGGAAAGCGCCGCT
*
86044 AAAGACCATGTTCTTTAGCG
66 AAAGACCATGTTCTTTAGCA
* * * *
86064 GCGTTTGTAG-GAAAGCGCCGTTAAAGAACATGGTCTTTAACG-GGGA-TTGT-GGGTAAGCGCC
1 GCGTTTGTAGAGAAAGCGCCGCTAAAGAAAAT-GTCTTT-A-GTGGCATTTGTGGGGAAAGCGCC
* *
86125 GCTAAAGACCATGTTCTATAGTA
63 GCTAAAGACCATGTTCTTTAGCA
86148 GCGTTT
1 GCGTTT
86154 TTTCACATAA
Statistics
Matches: 151, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
84 54 0.36
85 64 0.42
86 29 0.19
87 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (85 bp):
GCGTTTGTAGAGAAAGCGCCGCTAAAGAAAATGTCTTTAGTGGCATTTGTGGGGAAAGCGCCGCT
AAAGACCATGTTCTTTAGCA
Found at i:89032 original size:7 final size:6
Alignment explanation
Indices: 88999--89031 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
88989 TAAATTTGAA
88999 TATTTT TATTTT TATTTT TATTTT TAATTTT TA
1 TATTTT TATTTT TATTTT TATTTT T-ATTTT TA
89032 AAAGAATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:89497 original size:13 final size:13
Alignment explanation
Indices: 89473--89506 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
89463 TTTATTCCGA
*
89473 AATTTCTATAATT
1 AATTTTTATAATT
*
89486 ATTTTTTATAATT
1 AATTTTTATAATT
89499 AATTTTTA
1 AATTTTTA
89507 AGAATTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTTTTATAATT
Found at i:99216 original size:6 final size:6
Alignment explanation
Indices: 99192--99235 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
99182 ACAATTCATA
* * *
99192 TCACTT TCA-AT TCAATT TCACTT TCACTT TCATTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
99236 ATTTTGATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (6 bp):
TCACTT
Found at i:99222 original size:12 final size:11
Alignment explanation
Indices: 99186--99235 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
99176 CAATTTACAA
*
99186 TTCATATCACT
1 TTCATTTCACT
* *
99197 TTCAATTCAAT
1 TTCATTTCACT
99208 TTCACTTTCACT
1 TTCA-TTTCACT
99220 TTCATTTTCACT
1 TTCA-TTTCACT
99232 TTCA
1 TTCA
99236 ATTTTGATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 12 0.38
12 20 0.62
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (11 bp):
TTCATTTCACT
Found at i:99228 original size:18 final size:17
Alignment explanation
Indices: 99173--99238 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
99163 TAATAAGGAT
*
99173 TTTCAATTTACAATTC-A
1 TTTCACTTT-CAATTCAA
*
99190 TATCACTTTCAATTCAA
1 TTTCACTTTCAATTCAA
* *
99207 TTTCACTTTCACTTTCAT
1 TTTCACTTTCA-ATTCAA
99225 TTTCACTTTCAATT
1 TTTCACTTTCAATT
99239 TTGATCACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.15
17 20 0.49
18 15 0.37
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTCACTTTCAATTCAA
Found at i:103944 original size:86 final size:86
Alignment explanation
Indices: 103844--104111 Score: 256
Period size: 94 Copynumber: 3.0 Consensus size: 86
103834 TAAAGGGTGT
* * * *
103844 AAAAG-TCTTCAAACTTTTCCAAAAAAAAAAAACAATTAA-CTCTTTTTTTTATTTAATTAAGTA
1 AAAAGATCCTCAAACTTTT-CAAAAAAAAAAAACAATTAACCTCTTTTTTTCACTTAATTGAGTA
* * *
103907 CTTAAACTTTTAAAATGTATTA
65 CTTAAACTTTCAAAACGCATTA
* *
103929 AAAAGA-CACTCAAACTTTTTCTAAAAAAAAAAAGCAATTAAGCCCTTGCATTTTTTTCACTCAA
1 AAAAGATC-CTCAAAC-TTTTC-AAAAAAAAAAAACAATTAA--CC-T-C-TTTTTTTCACTTAA
*
103993 TTGTGTACTTAAAACTTTCAAAACGCATTA
58 TTGAGTACTT-AAACTTTCAAAACGCATTA
* * *
104023 AAAAGATCCTCAAACTTTT-AAAAAAAAAAAACAATTAAGCTCATTTTTGCACTTAATTGAGTAC
1 AAAAGATCCTCAAACTTTTCAAAAAAAAAAAACAATTAACCTCTTTTTTTCACTTAATTGAGTAC
* ** * *
104087 TTCAACTGGCAAAATGCATCA
66 TTAAACTTTCAAAACGCATTA
104108 AAAA
1 AAAA
104112 AACTTTTTGA
Statistics
Matches: 150, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
85 24 0.16
86 27 0.18
87 23 0.15
88 1 0.01
89 1 0.01
90 1 0.01
91 19 0.13
92 1 0.01
93 23 0.15
94 29 0.19
95 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (86 bp):
AAAAGATCCTCAAACTTTTCAAAAAAAAAAAACAATTAACCTCTTTTTTTCACTTAATTGAGTAC
TTAAACTTTCAAAACGCATTA
Found at i:104112 original size:86 final size:92
Alignment explanation
Indices: 103852--104112 Score: 201
Period size: 86 Copynumber: 2.9 Consensus size: 92
103842 GTAAAAGTCT
* * * *
103852 TCAAACTTTTCCAAAAAAAAAAAACAATTAA-CTCTT---TTTTTT--ATTTAATTAAGTACTT-
1 TCAAACTTTTCTAAAAAAAAAAAACAATTAAGC-CTTGCATTTTTTGCACTCAATTGAGTACTTA
*** * * *
103910 AAACTTTTAAAATGTATTAAAAAGACAC
65 AAACTGGCAAAACGCATAAAAAAGACAC
* * *
103938 TCAAACTTTTTCTAAAAAAAAAAAGCAATTAAGCCCTTGCATTTTTTTCACTCAATTGTGTACTT
1 TCAAAC-TTTTCTAAAAAAAAAAAACAATTAAG-CCTTGCATTTTTTGCACTCAATTGAGTACTT
** *
104003 AAAACTTTCAAAACGCATTAAAAAGATC-C
64 AAAACTGGCAAAACGCATAAAAAAGA-CAC
* *
104032 TCAAAC-TTT-TAAAAAAAAAAAACAATTAAG-C-T-CA-TTTTTGCACTTAATTGAGTACTT-C
1 TCAAACTTTTCTAAAAAAAAAAAACAATTAAGCCTTGCATTTTTTGCACTCAATTGAGTACTTAA
*
104090 AACTGGCAAAATGCATCAAAAAA
66 AACTGGCAAAACGCAT-AAAAAA
104113 ACTTTTTGAC
Statistics
Matches: 146, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
85 13 0.09
86 31 0.21
87 25 0.17
88 4 0.03
89 2 0.01
91 26 0.18
92 3 0.02
93 12 0.08
94 29 0.20
95 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (92 bp):
TCAAACTTTTCTAAAAAAAAAAAACAATTAAGCCTTGCATTTTTTGCACTCAATTGAGTACTTAA
AACTGGCAAAACGCATAAAAAAGACAC
Found at i:104280 original size:10 final size:10
Alignment explanation
Indices: 104265--104317 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
104255 ATAAGAATAT
104265 AAAAATTATA
1 AAAAATTATA
*
104275 AAAAATTGTA
1 AAAAATTATA
**
104285 AAATTTTAT-
1 AAAAATTATA
*
104294 AAAAATCATAA
1 AAAAATTAT-A
104305 AAAAATTATA
1 AAAAATTATA
104315 AAA
1 AAA
104318 TAGATAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 6 0.18
10 19 0.58
11 8 0.24
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:104324 original size:29 final size:29
Alignment explanation
Indices: 104263--104327 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
104253 ATATAAGAAT
* * **
104263 ATAAAAATTATAAAAAATTGTAAAATTTT
1 ATAAAAATCATAAAAAATTATAAAATTAG
104292 ATAAAAATCATAAAAAAATTATAAAA-TAG
1 ATAAAAATCAT-AAAAAATTATAAAATTAG
104321 ATAAAAA
1 ATAAAAA
104328 GCCATTTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (29 bp):
ATAAAAATCATAAAAAATTATAAAATTAG
Found at i:104573 original size:20 final size:19
Alignment explanation
Indices: 104498--104585 Score: 67
Period size: 18 Copynumber: 4.7 Consensus size: 19
104488 TACAAATTTT
*
104498 TTTTTTATATTTTATAAT-
1 TTTTATATATTTTATAATA
* * *
104516 TTTTTTATGACTTTATAAAA
1 TTTTATAT-ATTTTATAATA
* *
104536 GTTTATA-ATTTT-TTATA
1 TTTTATATATTTTATAATA
104553 TTTCTATATATTTTATAATA
1 TTT-TATATATTTTATAATA
104573 TTTT-TATGATTTT
1 TTTTATAT-ATTTT
104586 TATTTTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
17 5 0.09
18 19 0.35
19 19 0.35
20 12 0.22
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTATATATTTTATAATA
Found at i:104586 original size:20 final size:19
Alignment explanation
Indices: 104499--104618 Score: 65
Period size: 18 Copynumber: 6.5 Consensus size: 19
104489 ACAAATTTTT
*
104499 TTTTTATA-TTTTATAATT
1 TTTTTATATTTTTATAATA
*
104517 TTTTTATGA-CTTTATAA-A
1 TTTTTAT-ATTTTTATAATA
**
104535 AGTTTATAATTTTT-T-ATA
1 TTTTTAT-ATTTTTATAATA
*
104553 TTTCTATATATTTTATAATA
1 TTTTTATAT-TTTTATAATA
**
104573 TTTTTATGATTTTTATTTTA
1 TTTTTAT-ATTTTTATAATA
* *
104593 TTTCTAT-TTTTAATAA-A
1 TTTTTATATTTTTATAATA
*
104610 TTTATATAT
1 TTTTTATAT
104619 ATATTTATTA
Statistics
Matches: 77, Mismatches: 17, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
17 10 0.13
18 30 0.39
19 12 0.16
20 23 0.30
21 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATATTTTTATAATA
Found at i:105954 original size:12 final size:13
Alignment explanation
Indices: 105937--105969 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
105927 CCAAATAGGT
105937 TTTAAATGT-CAA
1 TTTAAATGTCCAA
105949 TTTAAATGTCCAA
1 TTTAAATGTCCAA
*
105962 TTAAAATG
1 TTTAAATG
105970 AGAACAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (13 bp):
TTTAAATGTCCAA
Found at i:111081 original size:29 final size:29
Alignment explanation
Indices: 111029--111458 Score: 381
Period size: 29 Copynumber: 14.8 Consensus size: 29
111019 GAGGGTCCCT
* * *
111029 AAACTATCTAAAAATTCCAATTTTACCCCT
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
*
111059 AAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
111089 AAACTTTCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCC-CA
* *
111118 GAACTTCCAAAAATCCCATTTTTGACCCC-
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
111147 GAACTTCCAAAAA-TCTCATTTTTACCCCC
1 AAACTTCCAAAAATTC-CATTTTTACCCCA
* ** * *
111176 GAACTTCCAAAAANCCCATTTCTAACCTCA
1 AAACTTCCAAAAATTCCATTT-TTACCCCA
*
111206 AAACTTCCAAAAATTACATTTTTACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
111235 AAACTTCC-AAAATTCCA-TTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * * *
111262 GAACTTCCAAAAATCCCATATTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
111291 AAACTTCCAAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
111320 GAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* * * *
111350 AAACTTCCAAAAGTTACATTTTTAGCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* ***
111379 GAACTTCC-AAAATTCCATTTTTGACATTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* * *
111408 AAACTTTCAAAAACTACCA-TTTTACCCCC
1 AAACTTCCAAAAA-TTCCATTTTTACCCCA
* *
111437 GAA-TGTCCAAAAACTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
111459 CGACCTCGAA
Statistics
Matches: 323, Mismatches: 62, Indels: 31
0.78 0.15 0.07
Matches are distributed among these distances:
27 16 0.05
28 38 0.12
29 174 0.54
30 91 0.28
31 4 0.01
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:111130 original size:59 final size:58
Alignment explanation
Indices: 111038--111458 Score: 408
Period size: 59 Copynumber: 7.2 Consensus size: 58
111028 TAAACTATCT
* * * *
111038 AAAAATTCCAATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTC
1 AAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTT-ACCCCAGAACTTCC
*
111097 AAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCC-GAACTTCC
1 AAAAATTCCATTTTTACCC-CAAAACTTCCAAAAATCCCATTTTT-ACCCCAGAACTTCC
** * * * *
111155 AAAAA-TCTCATTTTTACCCCCGAACTTCCAAAAANCCCATTTCTAACCTCAAAACTTCC
1 AAAAATTC-CATTTTTACCCCAAAACTTCCAAAAATCCCATTT-TTACCCCAGAACTTCC
* * *
111214 AAAAATTACATTTTTACCCCAAAACTTCC-AAAATTCCA-TTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTACCCCAGAACTTCC
* * * * * *
111270 AAAAATCCCATATTGACCCCAAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTACCCCAGAACTTCC
* * ** * *
111328 AAAAATCCCATTTTTGACCCCAAAACTTCCAAAAGTTACATTTTTAGCCCTGAACTTCC
1 AAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATCCCATTTTTACCCCAGAACTTCC
*** * * *
111387 -AAAATTCCATTTTTGACATTAAAACTTTCAAAAACTACCA-TTTTACCCCCGAA-TGTCC
1 AAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAA-TCCCATTTTTACCCCAGAACT-TCC
*
111445 AAAAACTCCATTTT
1 AAAAATTCCATTTT
111459 CGACCTCGAA
Statistics
Matches: 309, Mismatches: 41, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
56 37 0.12
57 14 0.05
58 126 0.41
59 130 0.42
60 2 0.01
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (58 bp):
AAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTACCCCAGAACTTCC
Found at i:111296 original size:144 final size:144
Alignment explanation
Indices: 111053--111399 Score: 500
Period size: 144 Copynumber: 2.4 Consensus size: 144
111043 TTCCAATTTT
* ** * *
111053 ACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAATTCCATTTTTACCCTC
1 ACCCCAAAACTTCCAAAAATTACATTTTT-ACCCCAAAAC-TTCCAAAATTCCA-TTTTACCCCC
* *
111118 GAACTTCCAAAAATCCCATTTTTGACCCCGAACTTCCAAAAA-TCTCATTTTTACCCCCGAACTT
63 GAACTTCCAAAAATCCCATTATTGACCCCAAACTTCCAAAAATTCT-ATTTTTACCCCCGAACTT
*
111182 CCAAAAANCCCATTTCTA
127 CCAAAAATCCCATTTCTA
*
111200 ACCTCAAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAATTCCATTTTACCCCCGAA
1 ACCCCAAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAATTCCATTTTACCCCCGAA
111265 CTTCCAAAAATCCCA-TATTGACCCCAAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCA
66 CTTCCAAAAATCCCATTATTGACCCC-AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCA
* *
111329 AAAATCCCATTTTTG
130 AAAATCCCATTTCTA
* * **
111344 ACCCCAAAACTTCCAAAAGTTACATTTTTAGCCCTGAACTTCCAAAATTCCATTTT
1 ACCCCAAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAATTCCATTTT
111400 TGACATTAAA
Statistics
Matches: 182, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
143 9 0.05
144 123 0.68
145 15 0.08
146 10 0.05
147 25 0.14
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (144 bp):
ACCCCAAAACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAATTCCATTTTACCCCCGAA
CTTCCAAAAATCCCATTATTGACCCCAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAA
AAATCCCATTTCTA
Done.