Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 94 of 226
Found at i:29473926 original size:18 final size:18
Alignment explanation
Indices: 29473905--29473974 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
29473895 GTATGCACTC
29473905 CATGCATTCCATGCAAAA
1 CATGCATTCCATGCAAAA
**
29473923 CATGCATTCCATGCAACC
1 CATGCATTCCATGCAAAA
* * * *
29473941 CATGTATTTCATACAAAT
1 CATGCATTCCATGCAAAA
*
29473959 CATGCATCCCATGCAA
1 CATGCATTCCATGCAA
29473975 TGTGCTGCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (18 bp):
CATGCATTCCATGCAAAA
Found at i:29473944 original size:36 final size:36
Alignment explanation
Indices: 29473904--29473974 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
29473894 GGTATGCACT
* *
29473904 CCATGCATTCCATGCAAAACATGCATTCCATGCAAC
1 CCATGCATTCCATACAAAACATGCATCCCATGCAAC
* * *
29473940 CCATGTATTTCATACAAATCATGCATCCCATGCAA
1 CCATGCATTCCATACAAAACATGCATCCCATGCAA
29473975 TGTGCTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (36 bp):
CCATGCATTCCATACAAAACATGCATCCCATGCAAC
Found at i:29479045 original size:10 final size:9
Alignment explanation
Indices: 29479011--29479051 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
29479001 CAATATTTGA
29479011 TTTA-TTAT
1 TTTATTTAT
29479019 TTTATTTGAT
1 TTTATTT-AT
29479029 TTTATTTAT
1 TTTATTTAT
29479038 TTTAATTT-T
1 TTT-ATTTAT
29479047 TTTAT
1 TTTAT
29479052 CTGACTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.20
9 11 0.37
10 13 0.43
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:29479450 original size:15 final size:16
Alignment explanation
Indices: 29479431--29479468 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
29479421 GAAAATACAA
29479431 AAAAAAAGAAAAAAAG
1 AAAAAAAGAAAAAAAG
*
29479447 AAAAAACG-AAAAAAG
1 AAAAAAAGAAAAAAAG
29479462 AAAAAAA
1 AAAAAAA
29479469 ATAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAG
Found at i:29479474 original size:8 final size:8
Alignment explanation
Indices: 29479431--29479468 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
29479421 GAAAATACAA
29479431 AAAAAAAG
1 AAAAAAAG
29479439 AAAAAAAG
1 AAAAAAAG
*
29479447 AAAAAACG
1 AAAAAAAG
29479455 -AAAAAAG
1 AAAAAAAG
29479462 AAAAAAA
1 AAAAAAA
29479469 ATAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:29480568 original size:21 final size:21
Alignment explanation
Indices: 29480522--29480569 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29480512 CTAATTGTCA
*
29480522 CTTTTGTTCATCAATTCTTTT
1 CTTTTGTTCATCAATTCTCTT
*
29480543 ATTTTGTTCATCAAATT-TCTT
1 CTTTTGTTCATC-AATTCTCTT
29480564 CTTTTG
1 CTTTTG
29480570 CTCCATTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (21 bp):
CTTTTGTTCATCAATTCTCTT
Found at i:29483973 original size:851 final size:851
Alignment explanation
Indices: 29482328--29484032 Score: 2948
Period size: 851 Copynumber: 2.0 Consensus size: 851
29482318 TCGTTTTAGG
* * * *
29482328 ATCACTTCAGTGGTCAATGTAACTTCTGAAATTCGGCTGAAACTTCTAGGTTGGGTTTTGGGGTG
1 ATCACTTCAGTGGTCAATGTAACTTCTGAAATCCGACTGAAACTTATAGGTTGGGTTTTGAGGTG
* *
29482393 CTATAATAAGGTTGATTAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
66 CTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
29482458 ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCCA
131 ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCCA
29482523 CCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTT
196 CCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTT
*
29482588 TCGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATTATG
261 TCGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATCATG
* *
29482653 CATTGAGTTGGTGGATTCAACTAGGAATTGATCGTCAAAGAAACCACGAAAGGGTAATTGAAACA
326 CATTGAGTTAGTGGATTCAACTAGGAATTGATCATCAAAGAAACCACGAAAGGGTAATTGAAACA
**
29482718 TGGGACAAGTTGAAGCAAATGATATGAAAGCGTTACGTTCTTCCTCATTACTATAGAGAGGTCTC
391 TGGGACAAGTTGAAGCAAATGATACAAAAGCGTTACGTTCTTCCTCATTACTATAGAGAGGTCTC
* *
29482783 AACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTCTTGATGAGTACTTTAAGGAGATAAAGA
456 AACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTCTTGATGAGTACTTTAAAGACATAAAGA
* * *
29482848 TGCTTATGCAAAGAGAAAATATACGAGAGGATGAAGAAACTACCATCGTGTAATTTATAGATGGC
521 TGCTTATGCAAAGAGAAAATATACGAGAGGACGAAGAAAATACCATCGTGCAATTTATAGATGGC
* * *
29482913 TTGAATATTTTGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACA
586 TTGAACAGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACA
*
29482978 CAAGACAATTGAGATTGAGCAACAATTTCAGCAACATTAATCTCGTCCATTTGGCGCATCACACT
651 CAAGACAATTGAGATTGAGCAACAATTTCAGCAACATCAATCTCGTCCATTTGGCGCATCACACT
29483043 ATTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATAAG
716 ATTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATAAG
* * * *
29483108 TTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGGAGCTCTTACAAAACATTC
781 TTATTTCAAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGAAGCTCCTACAAAACATTA
29483173 TACTAC
846 TACTAC
* *
29483179 ATCACTTTAGTGGTCAATGTAACCTT-TGAGATCCGACTGAAACTTATAGGTTGGGTTTTGAGGT
1 ATCACTTCAGTGGTCAATGTAA-CTTCTGAAATCCGACTGAAACTTATAGGTTGGGTTTTGAGGT
*
29483243 GTTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
65 GCTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
29483308 GATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCC
130 GATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCC
*
29483373 ACCATTTCGAGGGACGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGT
195 ACCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGT
*
29483438 TTCGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATTTTAAGATCAT
260 TTCGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATCAT
* * * *
29483503 GCATTGAGTTAGTGGATTTAACTTGGAATTGATCATCAAAGAAACCGCTAAAGGGTAATTGAAAC
325 GCATTGAGTTAGTGGATTCAACTAGGAATTGATCATCAAAGAAACCACGAAAGGGTAATTGAAAC
*
29483568 ATGGGACAAGTTGAAGCAAGTGATACAAAAGCGTTACGTTCCTT-CTCATTACTATAGAGAGGTC
390 ATGGGACAAGTTGAAGCAAATGATACAAAAGCGTTACGTT-CTTCCTCATTACTATAGAGAGGTC
*
29483632 TCAACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTGTTGATGAGTACTTTAAAGACATAAA
454 TCAACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTCTTGATGAGTACTTTAAAGACATAAA
* * * *
29483697 GATGCTTATGCAAAGGGCAAATATACGAGAGGACGAAGAAAATAGCA-CGGTGCAATTTGTAGAT
519 GATGCTTATGCAAAGAGAAAATATACGAGAGGACGAAGAAAATACCATC-GTGCAATTTATAGAT
*
29483761 GGCTTGAACGGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGT
583 GGCTTGAACAGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGT
* * *
29483826 ACACAAGACAATTGAGTTTGAGCAACAATTTCAGCAACGTCAATGTCGTCCATTTGGCGCATCAC
648 ACACAAGACAATTGAGATTGAGCAACAATTTCAGCAACATCAATCTCGTCCATTTGGCGCATCAC
*
29483891 ACTATTATCGAGGTACAAGTTCTAATTCTACTTTCAACAATTTGAAACCTTCTTATGCTATTAAT
713 ACTATTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAAT
*
29483956 AAGTTATTTCAAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGAAGCTCCTACAAAACA
778 AAGTTATTTCAAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGAAGCTCCTACAAAACA
*
29484021 TTATTCTAC
843 TTATACTAC
29484030 ATC
1 ATC
29484033 TTTCAAGGAA
Statistics
Matches: 805, Mismatches: 46, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
850 1 0.00
851 798 0.99
852 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (851 bp):
ATCACTTCAGTGGTCAATGTAACTTCTGAAATCCGACTGAAACTTATAGGTTGGGTTTTGAGGTG
CTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCCA
CCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTT
TCGTTACTATAAATTTTGGGAAGAGGAAAAAGTCCAATTGACGACCCTTGGATTTTAAGATCATG
CATTGAGTTAGTGGATTCAACTAGGAATTGATCATCAAAGAAACCACGAAAGGGTAATTGAAACA
TGGGACAAGTTGAAGCAAATGATACAAAAGCGTTACGTTCTTCCTCATTACTATAGAGAGGTCTC
AACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTCTTGATGAGTACTTTAAAGACATAAAGA
TGCTTATGCAAAGAGAAAATATACGAGAGGACGAAGAAAATACCATCGTGCAATTTATAGATGGC
TTGAACAGTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACA
CAAGACAATTGAGATTGAGCAACAATTTCAGCAACATCAATCTCGTCCATTTGGCGCATCACACT
ATTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATAAG
TTATTTCAAAAACATGCTGAGACTAAACCTTTTGAGTAGAAAAGTGAAGCTCCTACAAAACATTA
TACTAC
Found at i:29485993 original size:11 final size:11
Alignment explanation
Indices: 29485977--29486002 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29485967 TTCGCTGCCT
29485977 TATTATTCTAA
1 TATTATTCTAA
29485988 TATTATTCTAA
1 TATTATTCTAA
29485999 TATT
1 TATT
29486003 TGATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTATTCTAA
Found at i:29486029 original size:14 final size:13
Alignment explanation
Indices: 29486006--29486047 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
29485996 TAATATTTGA
29486006 TTTATTATTTTAT
1 TTTATTATTTTAT
29486019 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
*
29486032 TTTAATTGTTTTAT
1 TTT-ATTATTTTAT
29486046 TT
1 TT
29486048 AACTTGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:29489906 original size:22 final size:20
Alignment explanation
Indices: 29489857--29489906 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
29489847 GTTCACTTTT
29489857 ATATC-TTAAAATATAAAAA
1 ATATCATTAAAATATAAAAA
*
29489876 ATATTATTAAAATATAAAAAA
1 ATATCATTAAAATAT-AAAAA
29489897 ATATACATTA
1 ATAT-CATTA
29489907 GTCAAACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 9 0.35
22 4 0.15
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATCATTAAAATATAAAAA
Found at i:29490022 original size:19 final size:21
Alignment explanation
Indices: 29489981--29490022 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
29489971 AATGTGATAT
* *
29489981 TTAAAACTATACAAATTATCA
1 TTAAAACTATACAAATAAGCA
29490002 TTAAAA-TATA-AAATAAGCA
1 TTAAAACTATACAAATAAGCA
29490021 TT
1 TT
29490023 CACTACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAACTATACAAATAAGCA
Found at i:29490040 original size:120 final size:120
Alignment explanation
Indices: 29489814--29490044 Score: 268
Period size: 120 Copynumber: 1.9 Consensus size: 120
29489804 TTCGTAATCC
* * * * * * * *
29489814 ACACAAATCTAATTATTCAAACAAACATATAATGTTCACTTTTATATCTTAAAATATAAAAAATA
1 ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATATCTTAAAATATAAAAAATA
* * * * *
29489879 TTATTAAAATATAAAAAAATATACATTAGTCAAACCAATCTTAATATCACTTTCA
66 TCATTAAAATATAAAAAAACATACACTAGCCAAAACAATCTTAATATCACTTTCA
* *
29489934 ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATAT-TTAAAACTATACAAATT
1 ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATATCTTAAAA-TATAAAAAAT
* * *
29489998 ATCATTAAAATATAAAATAAGCATTCACTA-CCAAAACTATCTTAATA
65 ATCATTAAAATATAAAA-AAACATACACTAGCCAAAACAATCTTAATA
29490045 CACAATTCTA
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
119 6 0.07
120 77 0.85
121 8 0.09
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.32
Consensus pattern (120 bp):
ACACAAATATAATCATTCAAACAAAAATATAATGATAAATGTGATATCTTAAAATATAAAAAATA
TCATTAAAATATAAAAAAACATACACTAGCCAAAACAATCTTAATATCACTTTCA
Found at i:29492253 original size:3 final size:3
Alignment explanation
Indices: 29492245--29492272 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29492235 ACCCCTTTTT
29492245 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29492273 TAAAGAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:29492702 original size:18 final size:18
Alignment explanation
Indices: 29492658--29492703 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
29492648 TAAATAGATA
* *
29492658 TTAAACTTATTCATAAAT
1 TTAAATTTAATCATAAAT
*
29492676 TTAAAATTTAATCATGAAT
1 TT-AAATTTAATCATAAAT
29492695 TTAAATTTA
1 TTAAATTTA
29492704 TATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAAATTTAATCATAAAT
Found at i:29493803 original size:27 final size:28
Alignment explanation
Indices: 29493745--29493797 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
29493735 TTGAATCTAA
* *
29493745 AAAAATTGTTTGAAAATTAAAAAAATAT
1 AAAAATTGTTAGAAAATAAAAAAAATAT
29493773 AAAAATT-TTAGAAAATAAAAAAAAT
1 AAAAATTGTTAGAAAATAAAAAAAAT
29493798 TCAAAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (28 bp):
AAAAATTGTTAGAAAATAAAAAAAATAT
Found at i:29495663 original size:23 final size:24
Alignment explanation
Indices: 29495637--29495695 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
29495627 TTTTAAAACT
29495637 TTATATATTTTTTGAAT-TTTAAA
1 TTATATATTTTTTGAATGTTTAAA
* *
29495660 TTATATATATATTTGAATGTTTAAG
1 TTATATAT-TTTTTGAATGTTTAAA
29495685 TTATATATTTT
1 TTATATATTTT
29495696 CGAATAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.26
24 10 0.32
25 13 0.42
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (24 bp):
TTATATATTTTTTGAATGTTTAAA
Found at i:29495700 original size:23 final size:22
Alignment explanation
Indices: 29495637--29495700 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
29495627 TTTTAAAACT
29495637 TTATATATTTTTTGAATTTTAAA
1 TTATATA-TTTTTGAATTTTAAA
*
29495660 TTATATATATATTTGAATGTTTAAG
1 TTATATAT-T-TTTGAAT-TTTAAA
*
29495685 TTATATATTTTCGAAT
1 TTATATATTTTTGAAT
29495701 AATTTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 1 0.03
23 14 0.39
24 8 0.22
25 13 0.36
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (22 bp):
TTATATATTTTTGAATTTTAAA
Found at i:29499322 original size:40 final size:40
Alignment explanation
Indices: 29499236--29499384 Score: 163
Period size: 40 Copynumber: 3.7 Consensus size: 40
29499226 CACACCAGTT
* * * * * *
29499236 TGTGGACAAGCCACCAGTATTACATATAAACTGTCAGTAA
1 TGTGGACAAGCCACCAGAATTGCAAACAAATTGACAGTAA
* * * *
29499276 TATGGACAAGCCACCAGAATTGCAAACAAATTTATAGTAT
1 TGTGGACAAGCCACCAGAATTGCAAACAAATTGACAGTAA
* * * *
29499316 TGTGGACAAGCCACTAAAATTGCAAACAAGTTGCCAGTAA
1 TGTGGACAAGCCACCAGAATTGCAAACAAATTGACAGTAA
*
29499356 TGTGGACAAGCCACCAGAATTGCAGACAA
1 TGTGGACAAGCCACCAGAATTGCAAACAA
29499385 CCTACTAGTA
Statistics
Matches: 88, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 88 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (40 bp):
TGTGGACAAGCCACCAGAATTGCAAACAAATTGACAGTAA
Found at i:29501440 original size:25 final size:26
Alignment explanation
Indices: 29501385--29501440 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
29501375 AAATGTTAAG
29501385 TAAATATATTATATTATTATATATAA
1 TAAATATATTATATTATTATATATAA
*
29501411 T-AATATATTATGTTATTATA-ATAA
1 TAAATATATTATATTATTATATATAA
29501435 TAAATA
1 TAAATA
29501441 AATAAAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 5 0.18
25 22 0.79
26 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAATATATTATATTATTATATATAA
Found at i:29507769 original size:15 final size:15
Alignment explanation
Indices: 29507749--29507791 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
29507739 TGTTAAGTAA
29507749 ATATATTATATTATT
1 ATATATTATATTATT
29507764 ATATA-TA-A-TA--
1 ATATATTATATTATT
29507774 ATATATTATATTATT
1 ATATATTATATTATT
29507789 ATA
1 ATA
29507792 AAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 5 0.22
11 2 0.09
12 3 0.13
13 3 0.13
14 2 0.09
15 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATTATATTATT
Found at i:29507897 original size:27 final size:27
Alignment explanation
Indices: 29507809--29507900 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
29507799 AAATAAATAA
* *
29507809 AAAGAAAAAGGAAATAGAA-AAAGAAGG
1 AAAGAAAAA-GAAAGAAAAGAAAGAAGG
* *
29507836 AAAGAAACAGAGAAAGCCAAACGAAA-CAGG
1 AAAGAAA-A-AGAAAG--AAAAGAAAGAAGG
*
29507866 -GAGAAAAAGAAAGAAAAGAAAGAAGG
1 AAAGAAAAAGAAAGAAAAGAAAGAAGG
29507892 AAAGAAAAA
1 AAAGAAAAA
29507901 TTAGGGTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
25 7 0.14
26 3 0.06
27 20 0.40
28 6 0.12
29 6 0.12
30 5 0.10
31 3 0.06
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.01
Consensus pattern (27 bp):
AAAGAAAAAGAAAGAAAAGAAAGAAGG
Found at i:29512314 original size:24 final size:24
Alignment explanation
Indices: 29512285--29512341 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
29512275 GTTATTACTG
29512285 TTTTGATGAGAACTTTGTAGGTGT
1 TTTTGATGAGAACTTTGTAGGTGT
*
29512309 TTTTGATGAGACCTTTGTAGGTGT
1 TTTTGATGAGAACTTTGTAGGTGT
29512333 TTTTGATGA
1 TTTTGATGA
29512342 AAGTTCAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.28, T:0.47
Consensus pattern (24 bp):
TTTTGATGAGAACTTTGTAGGTGT
Found at i:29525160 original size:25 final size:25
Alignment explanation
Indices: 29525132--29525186 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29525122 TCAGTACAGT
*
29525132 CTATCTATAGTAGTCTCAATATATA
1 CTATCTATAGTAGTCTCAAGATATA
* * *
29525157 CTATGTATAGTAGTTTCAGGATATA
1 CTATCTATAGTAGTCTCAAGATATA
29525182 CTATC
1 CTATC
29525187 AAAAACAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (25 bp):
CTATCTATAGTAGTCTCAAGATATA
Found at i:29526553 original size:17 final size:18
Alignment explanation
Indices: 29526519--29526554 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
29526509 CATGTTGTTG
29526519 GCTCGTGTAGGCCCACAC
1 GCTCGTGTAGGCCCACAC
*
29526537 GCTCGTGT-GGCCTACAC
1 GCTCGTGTAGGCCCACAC
29526554 G
1 G
29526555 GCCCAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.36, G:0.31, T:0.19
Consensus pattern (18 bp):
GCTCGTGTAGGCCCACAC
Found at i:29539201 original size:16 final size:17
Alignment explanation
Indices: 29539180--29539213 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29539170 ATTATTTTGG
*
29539180 ATTTTTGG-GTATTTCC
1 ATTTTTGGTATATTTCC
29539196 ATTTTTGGTATATTTCC
1 ATTTTTGGTATATTTCC
29539213 A
1 A
29539214 GTCAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.56
Consensus pattern (17 bp):
ATTTTTGGTATATTTCC
Found at i:29543392 original size:208 final size:208
Alignment explanation
Indices: 29543034--29543469 Score: 847
Period size: 208 Copynumber: 2.1 Consensus size: 208
29543024 TTAAGAGGAA
29543034 GCGCCGCAAAATGTTTTAAGCATACGACGTCGTTTCCTGTTGTGCTTAGGGACATTAGTGGCGCT
1 GCGCCGCAAAATGTTTTAAGCATACGACGTCGTTTCCTGTTGTGCTTAGGGACATTAGTGGCGCT
29543099 TTGCGAAAAATGCCGCAAATGTCAAGCACTAGCGGTAATAGTTTTAGGAAAACGACATCGTTTTA
66 TTGCGAAAAATGCCGCAAATGTCAAGCACTAGCGGTAATAGTTTTAGGAAAACGACATCGTTTTA
29543164 TTTTTCAAATTTTAGAGATATTAGTGGCGCGTAGCTATAAACGCTGCAAAGTTTAATAATTAGCA
131 TTTTTCAAATTTTAGAGATATTAGTGGCGCGTAGCTATAAACGCTGCAAAGTTTAATAATTAGCA
29543229 GCGCTTTTACGTT
196 GCGCTTTTACGTT
29543242 GCGCCGCAAAATGTTTTAAGCATACGACGTCGTTTCCTGTTGTGCTTAGGGACATTAGTGGCGCT
1 GCGCCGCAAAATGTTTTAAGCATACGACGTCGTTTCCTGTTGTGCTTAGGGACATTAGTGGCGCT
29543307 TTGCGAAAAATGCCGCAAATGTCAAGCACTAGCGGTAATAGTTTTAGGAAAACGACATCGTTTTA
66 TTGCGAAAAATGCCGCAAATGTCAAGCACTAGCGGTAATAGTTTTAGGAAAACGACATCGTTTTA
29543372 TTTTTCAAATTTTAGAGATATTAGTGGCGCGTAGCTATAAACGCTGCAAAGTTTAATAATTAGCA
131 TTTTTCAAATTTTAGAGATATTAGTGGCGCGTAGCTATAAACGCTGCAAAGTTTAATAATTAGCA
29543437 GCGCTTTTACGTT
196 GCGCTTTTACGTT
* *
29543450 GCGCCGTAAAA-CTTTTAAGC
1 GCGCCGCAAAATGTTTTAAGC
29543470 GAACGGCAAC
Statistics
Matches: 226, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
207 8 0.04
208 218 0.96
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (208 bp):
GCGCCGCAAAATGTTTTAAGCATACGACGTCGTTTCCTGTTGTGCTTAGGGACATTAGTGGCGCT
TTGCGAAAAATGCCGCAAATGTCAAGCACTAGCGGTAATAGTTTTAGGAAAACGACATCGTTTTA
TTTTTCAAATTTTAGAGATATTAGTGGCGCGTAGCTATAAACGCTGCAAAGTTTAATAATTAGCA
GCGCTTTTACGTT
Found at i:29543546 original size:7 final size:7
Alignment explanation
Indices: 29543534--29543560 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29543524 GGGGTTTAAT
29543534 GGTTTAG
1 GGTTTAG
29543541 GGTTTAG
1 GGTTTAG
29543548 GGTTTAG
1 GGTTTAG
29543555 GGTTTA
1 GGTTTA
29543561 AGATTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:29543567 original size:14 final size:14
Alignment explanation
Indices: 29543525--29543567 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
29543515 GGGGTTCATG
29543525 GGGTTTAATGGTTTA
1 GGGTTTAA-GGTTTA
*
29543540 GGGTTTAGGGTTTA
1 GGGTTTAAGGTTTA
*
29543554 GGGTTTAAGATTTA
1 GGGTTTAAGGTTTA
29543568 TGATTTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (14 bp):
GGGTTTAAGGTTTA
Found at i:29543575 original size:29 final size:29
Alignment explanation
Indices: 29543543--29543609 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
29543533 TGGTTTAGGG
**
29543543 TTTAGGGTTTAGGGTTTAAGATTTATGAT
1 TTTAGGGTTTAGAATTTAAGATTTATGAT
* * *
29543572 TTTAGGGTTTATAATTTATGATTTATGGT
1 TTTAGGGTTTAGAATTTAAGATTTATGAT
29543601 TTTAGGGTT
1 TTTAGGGTT
29543610 AATTTATGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.52
Consensus pattern (29 bp):
TTTAGGGTTTAGAATTTAAGATTTATGAT
Found at i:29543604 original size:22 final size:22
Alignment explanation
Indices: 29543550--29543595 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
29543540 GGGTTTAGGG
29543550 TTTAGGGTTTA-AGATTTATGAT
1 TTTAGGGTTTATA-ATTTATGAT
29543572 TTTAGGGTTTATAATTTATGAT
1 TTTAGGGTTTATAATTTATGAT
29543594 TT
1 TT
29543596 ATGGTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (22 bp):
TTTAGGGTTTATAATTTATGAT
Found at i:29543762 original size:22 final size:22
Alignment explanation
Indices: 29543737--29543787 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
29543727 TGTTTAGGGT
*
29543737 TTAAGAGG-TTAAAGTTTAAAGG
1 TTAAG-GGTTTAAAGTCTAAAGG
*
29543759 TTAAGGGTTTAAAGTCTAAGGG
1 TTAAGGGTTTAAAGTCTAAAGG
29543781 TTAAGGG
1 TTAAGGG
29543788 CTTATGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.31
Consensus pattern (22 bp):
TTAAGGGTTTAAAGTCTAAAGG
Found at i:29543768 original size:15 final size:15
Alignment explanation
Indices: 29543732--29543782 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
29543722 TTTATTGTTT
29543732 AGGGTTTAAGAGGTTA
1 AGGGTTTAA-AGGTTA
*
29543748 A-AGTTTAAAGGTTA
1 AGGGTTTAAAGGTTA
29543762 AGGGTTTAAA-GTCTA
1 AGGGTTTAAAGGT-TA
29543777 AGGGTT
1 AGGGTT
29543783 AAGGGCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.29
15 21 0.68
16 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (15 bp):
AGGGTTTAAAGGTTA
Found at i:29543863 original size:23 final size:23
Alignment explanation
Indices: 29543832--29543877 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29543822 ATTTAAGGGT
* *
29543832 TATGCTAAAAATATAGAAAAATA
1 TATGCTAAAAATAGAAAAAAATA
*
29543855 TATGTTAAAAATAGAAAAAAATA
1 TATGCTAAAAATAGAAAAAAATA
29543878 AAATAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (23 bp):
TATGCTAAAAATAGAAAAAAATA
Found at i:29544350 original size:115 final size:116
Alignment explanation
Indices: 29543997--29544456 Score: 464
Period size: 115 Copynumber: 4.0 Consensus size: 116
29543987 TTTGTCTGAT
* * * * * * * *
29543997 TTTTTGGTGGCGTTTTTTCTAAAATGCCGCAAAAGGAGT-TATATTAGTGGTGTTTCTACGAAAA
1 TTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGA-TATGTGTTAGTGGCGTTTTTACTAAAA
* ** * *
29544061 ACGCCGCAATTATGTTTTTTTGTCTTTGTTAAACGTTGTCGTTTTTATCTACG
65 ACGCCGCAATTATG-TTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACG
* * * * **
29544114 TTTTCAGTGGCGTTTTTTCCAAAACGCCGCAAAATGATATGTGTTAGTGGCG-TTTT-C-AGGTA
1 TTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGTTAGTGGCGTTTTTACTA-AAA
* * * *
29544176 ACGCCGCAATTATGTTATTAGTCTTTTG-TAAACGTTGTTGTTTTTATCTACA
65 ACGCCGCAATTATGTTATAAGT-GTTTGCTAAACGTTGTCGTTTTTATCTACG
* * * * * *
29544228 TTATTAGTGGCATTTTTACAAAAATGCCGCAAAAGGTTATGTGGTAGTGGCGTTTTTA-TAAAAA
1 TTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGTTAGTGGCGTTTTTACTAAAAA
* *
29544292 TGCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTTTATTTACG
66 CGCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACG
* ** * * * * *
29544343 TTTTTAGTGGCGTTTGTACTAAAACGCCGGTAAAGGATATGTTTTCGTGGCATTTTTATTATAAA
1 TTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGTTAGTGGCGTTTTTACTAAAAA
* *
29544408 CGCCGCAATTATGTTTTAAGTGTTTGCTAAACGTTGTTGTTTTCTATCT
66 CGCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTT-TATCT
29544457 GGGATTTTTT
Statistics
Matches: 284, Mismatches: 50, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
114 76 0.27
115 112 0.39
116 50 0.18
117 46 0.16
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.42
Consensus pattern (116 bp):
TTTTTAGTGGCGTTTTTACTAAAACGCCGCAAAAGGATATGTGTTAGTGGCGTTTTTACTAAAAA
CGCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCGTTTTTATCTACG
Found at i:29544638 original size:23 final size:21
Alignment explanation
Indices: 29544573--29544638 Score: 51
Period size: 23 Copynumber: 2.9 Consensus size: 21
29544563 CCACTCTGAT
*
29544573 TTCCCCAATTTCATTTCCCTAA
1 TTCCCC-ATTTCATTTCCCCAA
* **
29544595 TTTCCCATTTCCTATGGCCCCAA
1 TTCCCCATTT-C-ATTTCCCCAA
29544618 CTTCCCCGATTTCATTTCCCC
1 -TTCCCC-ATTTCATTTCCCC
29544639 TCAATTCTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
21 4 0.12
22 6 0.18
23 13 0.39
24 6 0.18
25 4 0.12
ACGTcount: A:0.17, C:0.41, G:0.05, T:0.38
Consensus pattern (21 bp):
TTCCCCATTTCATTTCCCCAA
Found at i:29546372 original size:12 final size:12
Alignment explanation
Indices: 29546355--29546380 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29546345 TTCTTAATAA
29546355 TTATATATAAGC
1 TTATATATAAGC
29546367 TTATATATAAGC
1 TTATATATAAGC
29546379 TT
1 TT
29546381 GCATAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTATATATAAGC
Found at i:29546398 original size:12 final size:12
Alignment explanation
Indices: 29546383--29546471 Score: 54
Period size: 12 Copynumber: 8.2 Consensus size: 12
29546373 ATAAGCTTGC
29546383 ATAACTTACATA
1 ATAACTTACATA
29546395 ATAACTTAC---
1 ATAACTTACATA
*
29546404 ATAACTTATAT-
1 ATAACTTACATA
*
29546415 ATAA-TAACATA
1 ATAACTTACATA
29546426 ATAACTT--A-A
1 ATAACTTACATA
* *
29546435 GTAACTTATAT-
1 ATAACTTACATA
*
29546446 ATAA-TAACATA
1 ATAACTTACATA
*
29546457 ATAAATTACATA
1 ATAACTTACATA
29546469 ATA
1 ATA
29546472 CATAACTTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
9 15 0.25
10 9 0.15
11 16 0.27
12 19 0.32
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:29546407 original size:9 final size:9
Alignment explanation
Indices: 29546395--29547295 Score: 539
Period size: 9 Copynumber: 103.4 Consensus size: 9
29546385 AACTTACATA
29546395 ATAACTTAC
1 ATAACTTAC
*
29546404 ATAACTTAT
1 ATAACTTAC
29546413 AT-A--TA-
1 ATAACTTAC
*
29546418 ATAACATA-
1 ATAACTTAC
29546426 ATAACTTA-
1 ATAACTTAC
*
29546434 AGTAACTTAT
1 A-TAACTTAC
29546444 AT-A--TA-
1 ATAACTTAC
*
29546449 ATAACATA-
1 ATAACTTAC
*
29546457 ATAAATTAC
1 ATAACTTAC
29546466 ATAA--TAC
1 ATAACTTAC
*
29546473 ATAACTTATAT
1 ATAAC-T-TAC
*
29546484 ATAAGCTTGC
1 ATAA-CTTAC
29546494 ATAACTTAC
1 ATAACTTAC
29546503 ATAA--TAC
1 ATAACTTAC
***
29546510 GCCACTTAC
1 ATAACTTAC
29546519 ATAACTTAC
1 ATAACTTAC
*
29546528 ATAGCTTAC
1 ATAACTTAC
*
29546537 AT-TC-TAC
1 ATAACTTAC
*
29546544 ACAACTTAC
1 ATAACTTAC
*
29546553 ATAACATAC
1 ATAACTTAC
29546562 ATAA--TAC
1 ATAACTTAC
*
29546569 AGAACTTAC
1 ATAACTTAC
**
29546578 ATAAAATAC
1 ATAACTTAC
29546587 --AACTTAC
1 ATAACTTAC
*
29546594 ATATCTTAC
1 ATAACTTAC
29546603 ATAA--TAC
1 ATAACTTAC
29546610 ATAACTTAC
1 ATAACTTAC
29546619 ATAA--TAC
1 ATAACTTAC
*
29546626 A-ACATTTAC
1 ATA-ACTTAC
* *
29546635 ACAACTTAA
1 ATAACTTAC
*
29546644 ATAACTTAT
1 ATAACTTAC
*
29546653 ATAACTTGC
1 ATAACTTAC
*
29546662 ATAACTTAT
1 ATAACTTAC
*
29546671 ATAA-TAAC
1 ATAACTTAC
*
29546679 ATAATAACTAAC
1 ---ATAACTTAC
** *
29546691 ATAAAATAT
1 ATAACTTAC
*
29546700 ATAAACATATAT
1 AT-AAC-T-TAC
* *
29546712 AGAAACTTGC
1 A-TAACTTAC
*
29546722 ATAACTTAT
1 ATAACTTAC
*
29546731 ATAA-TAAC
1 ATAACTTAC
*
29546739 ATAA-TAAC
1 ATAACTTAC
29546747 -TAACATAATAC
1 ATAAC-T--TAC
29546758 ATAACTTAC
1 ATAACTTAC
29546767 ATAACTTAC
1 ATAACTTAC
*
29546776 ATAAATTA-
1 ATAACTTAC
29546784 AGTAACTTAC
1 A-TAACTTAC
29546794 ATAACTTAC
1 ATAACTTAC
29546803 ATAACTTAC
1 ATAACTTAC
* *
29546812 ATAAATTAA
1 ATAACTTAC
29546821 ATAACTTAC
1 ATAACTTAC
29546830 ATAACTTAC
1 ATAACTTAC
29546839 ATAACTTAC
1 ATAACTTAC
29546848 ATAACTTAC
1 ATAACTTAC
* *
29546857 ATAAATTAA
1 ATAACTTAC
29546866 ATAACTTAC
1 ATAACTTAC
29546875 ATAACTTAC
1 ATAACTTAC
*
29546884 ATAACTTAA
1 ATAACTTAC
29546893 ATAACTTAC
1 ATAACTTAC
29546902 ATAA--TAC
1 ATAACTTAC
29546909 ATAACCTT-C
1 ATAA-CTTAC
*
29546918 CTAACTTAC
1 ATAACTTAC
* *
29546927 ATTATTTAC
1 ATAACTTAC
29546936 ATAA--TAC
1 ATAACTTAC
* *
29546943 A-ATGCCTAC
1 ATA-ACTTAC
29546952 ATAACTTAC
1 ATAACTTAC
29546961 ATAACTTAC
1 ATAACTTAC
* *
29546970 ATAAATTAA
1 ATAACTTAC
29546979 ATAACTTAC
1 ATAACTTAC
29546988 ATAACTTAC
1 ATAACTTAC
*
29546997 ATAACTTAA
1 ATAACTTAC
*
29547006 ATAACTTAA
1 ATAACTTAC
29547015 ATAACTTAC
1 ATAACTTAC
29547024 ATAA--TAC
1 ATAACTTAC
29547031 ATAACCTT-C
1 ATAA-CTTAC
*
29547040 CTAACTTAC
1 ATAACTTAC
* *
29547049 ATTATTTAC
1 ATAACTTAC
29547058 ATAA--TAC
1 ATAACTTAC
** **
29547065 ATTGCCCAC
1 ATAACTTAC
29547074 ATAACTTAC
1 ATAACTTAC
29547083 ATAACTTAC
1 ATAACTTAC
* *
29547092 ATAAATTAA
1 ATAACTTAC
29547101 ATAACTTAC
1 ATAACTTAC
29547110 ATAACTTAC
1 ATAACTTAC
*
29547119 ATAACTTAA
1 ATAACTTAC
29547128 ATAACTTAC
1 ATAACTTAC
29547137 ATAA--TAC
1 ATAACTTAC
29547144 ATAACCTT-C
1 ATAA-CTTAC
*
29547153 TTAACTTAC
1 ATAACTTAC
*
29547162 ATTA--TAC
1 ATAACTTAC
*
29547169 ACAACTTAC
1 ATAACTTAC
29547178 ATAA-TTA-
1 ATAACTTAC
*
29547185 AT-ATTATAC
1 ATAACT-TAC
* *
29547194 ACAATTTAC
1 ATAACTTAC
29547203 ATAA--TAC
1 ATAACTTAC
*
29547210 ATTACTTAC
1 ATAACTTAC
29547219 ATAACTTAC
1 ATAACTTAC
*
29547228 ATTACTTAC
1 ATAACTTAC
29547237 AGT-ACTTTAC
1 A-TAAC-TTAC
29547247 TTATAGTACTTAC
1 --ATA--ACTTAC
*
29547260 GTAA--TAC
1 ATAACTTAC
29547267 ATAA--TAC
1 ATAACTTAC
29547274 ATAACTTAC
1 ATAACTTAC
29547283 ATAACTTAC
1 ATAACTTAC
29547292 ATAA
1 ATAA
29547296 TACATAAAAA
Statistics
Matches: 704, Mismatches: 110, Indels: 156
0.73 0.11 0.16
Matches are distributed among these distances:
5 4 0.01
6 9 0.01
7 98 0.14
8 49 0.07
9 479 0.68
10 24 0.03
11 18 0.03
12 17 0.02
13 4 0.01
14 2 0.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:29546425 original size:31 final size:31
Alignment explanation
Indices: 29546390--29546469 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
29546380 TGCATAACTT
29546390 ACATAATAACTTACATAACTTATATATAATA
1 ACATAATAACTTACATAACTTATATATAATA
29546421 ACATAATAACTTA-AGTAACTTATATATAATA
1 ACATAATAACTTACA-TAACTTATATATAATA
*
29546452 ACATAATAAATTACATAA
1 ACATAATAACTTACATAA
29546470 TACATAACTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (31 bp):
ACATAATAACTTACATAACTTATATATAATA
Found at i:29546453 original size:23 final size:23
Alignment explanation
Indices: 29546423--29546480 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
29546413 ATATAATAAC
* *
29546423 ATAATAACTTAAGTAACTTATAT-
1 ATAATAACTTAA-TAAATTACATA
*
29546446 ATAATAACATAATAAATTACATA
1 ATAATAACTTAATAAATTACATA
29546469 ATACATAACTTA
1 ATA-ATAACTTA
29546481 TATATAAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 8 0.28
23 14 0.48
24 7 0.24
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.34
Consensus pattern (23 bp):
ATAATAACTTAATAAATTACATA
Found at i:29546544 original size:25 final size:25
Alignment explanation
Indices: 29546516--29546587 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
29546506 ATACGCCACT
* * * **
29546516 TACATAACTTACATAGCTTACATTC
1 TACACAACTTACATAACATACATAA
29546541 TACACAACTTACATAACATACATAA
1 TACACAACTTACATAACATACATAA
* *
29546566 TACAGAACTTACATAAAATACA
1 TACACAACTTACATAACATACA
29546588 ACTTACATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (25 bp):
TACACAACTTACATAACATACATAA
Found at i:29546579 original size:41 final size:41
Alignment explanation
Indices: 29546542--29546622 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
29546532 CTTACATTCT
29546542 ACACAACTTACATAACATACATAATACAGAACTTACATAAA
1 ACACAACTTACATAACATACATAATACAGAACTTACATAAA
* * * *
29546583 ATACAACTTACATATCTTACATAATACATAACTTACATAA
1 ACACAACTTACATAACATACATAATACAGAACTTACATAA
29546623 TACAACATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.51, C:0.21, G:0.01, T:0.27
Consensus pattern (41 bp):
ACACAACTTACATAACATACATAATACAGAACTTACATAAA
Found at i:29546601 original size:25 final size:25
Alignment explanation
Indices: 29546573--29546621 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29546563 TAATACAGAA
*
29546573 CTTACATAAAATACAACTTACATAT
1 CTTACATAAAACACAACTTACATAT
* *
29546598 CTTACATAATACATAACTTACATA
1 CTTACATAAAACACAACTTACATA
29546622 ATACAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (25 bp):
CTTACATAAAACACAACTTACATAT
Found at i:29546693 original size:29 final size:30
Alignment explanation
Indices: 29546643--29546754 Score: 106
Period size: 29 Copynumber: 3.8 Consensus size: 30
29546633 ACACAACTTA
* **
29546643 AATAACTTATATAACTTGCATAACTTATAT
1 AATAACATATATAACTAACATAACTTATAT
**
29546673 AATAACATA-ATAACTAACATAAAATATAT
1 AATAACATATATAACTAACATAACTTATAT
**
29546702 -A-AACATATATAGAAACTTGCATAACTTATAT
1 AATAACATATAT---AACTAACATAACTTATAT
29546733 AATAACATA-ATAACTAACATAA
1 AATAACATATATAACTAACATAA
29546755 TACATAACTT
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
27 6 0.09
28 3 0.05
29 25 0.38
30 8 0.12
31 14 0.22
32 3 0.05
33 6 0.09
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (30 bp):
AATAACATATATAACTAACATAACTTATAT
Found at i:29546923 original size:34 final size:34
Alignment explanation
Indices: 29546449--29547237 Score: 398
Period size: 34 Copynumber: 23.3 Consensus size: 34
29546439 CTTATATATA
* * *
29546449 ATAACATA-ATAAATTACATAATACATAACTTATAT
1 ATAACTTACATAACTTACATAATACATAAC-T-TAC
* ***
29546484 ATAAGCTTGCATAACTTACATAATACGCCACTTAC
1 ATAA-CTTACATAACTTACATAATACATAACTTAC
* ** *
29546519 ATAACTTACATAGCTTACATTCTACACAACTTAC
1 ATAACTTACATAACTTACATAATACATAACTTAC
* * **
29546553 ATAACATACATAA--TACAGAACTTACATAAAATAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
*
29546587 --AACTTACATATCTTACATAATACATAACTTAC
1 ATAACTTACATAACTTACATAATACATAACTTAC
* * * *
29546619 ATAA--TACA-ACATTTACACAACTTAAATAACTTAT
1 ATAACTTACATA-ACTTACATAA--TACATAACTTAC
* *
29546653 ATAACTTGCATAACTT--AT-ATA-ATAACATA-
1 ATAACTTACATAACTTACATAATACATAACTTAC
* ** * *
29546682 ATAACTAACATAAAATATATAA-ACAT-A-TATAG
1 ATAACTTACATAACTTACATAATACATAACT-TAC
* *
29546714 A-AACTTGCATAACTT--AT-ATA-ATAACATA-
1 ATAACTTACATAACTTACATAATACATAACTTAC
*
29546742 ATAACTAACATAA--TACATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
*
29546776 ATAAATTA-AGTAACTTACATAACTTACATAACTTAC
1 ATAACTTACA-TAACTTACATAA--TACATAACTTAC
* *
29546812 ATAAATTAAATAACTTACATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
* *
29546848 ATAACTTACATAAATTAAATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
*
29546884 ATAACTTAAATAACTTACATAATACATAACCTT-C
1 ATAACTTACATAACTTACATAATACATAA-CTTAC
* * * * *
29546918 CTAACTTACATTATTTACATAATACA-ATGCCTAC
1 ATAACTTACATAACTTACATAATACATA-ACTTAC
*
29546952 ATAACTTACATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAACTTACAT-AA-TACATAACTTAC
* *
29546988 ATAACTTACATAACTTAAATAACTTAAATAACTTAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
* * *
29547024 ATAA--TACATAACCTT-CCTAACTTACATTATTTAC
1 ATAACTTACATAA-CTTACATAA--TACATAACTTAC
** **
29547058 ATAA--TACATTGCCCACATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
* * *
29547092 ATAAATTAAATAACTTACATAACTTACATAACTTAA
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
* *
29547128 ATAACTTACATAA--TACATAACCTTCTTAACTTAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
* * *
29547162 ATTA--TACACAACTTACATAATTA-AT-ATTATAC
1 ATAACTTACATAACTTACATAA-TACATAACT-TAC
* * *
29547194 ACAATTTACATAA--TACATTACTTACATAACTTAC
1 ATAACTTACATAACTTACA-TA-ATACATAACTTAC
*
29547228 ATTACTTACA
1 ATAACTTACA
29547238 GTACTTTACT
Statistics
Matches: 591, Mismatches: 108, Indels: 111
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.00
28 4 0.01
29 29 0.05
30 8 0.01
31 21 0.04
32 56 0.09
33 18 0.03
34 219 0.37
35 22 0.04
36 193 0.33
37 20 0.03
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (34 bp):
ATAACTTACATAACTTACATAATACATAACTTAC
Found at i:29552542 original size:54 final size:54
Alignment explanation
Indices: 29552460--29552567 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
29552450 TAACTATGTG
29552460 ATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTACGAAGCGATTGC
1 ATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTACGAAGCGATTGC
29552514 ATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTACGAAGCGATTGC
1 ATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTACGAAGCGATTGC
29552568 TTCTAGTGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (54 bp):
ATTTATTTATTAGGAAAAACTAAAGGATAAAAAGGCGGAGTACGAAGCGATTGC
Found at i:29552858 original size:21 final size:20
Alignment explanation
Indices: 29552832--29552882 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
29552822 TACAACTTAC
* *
29552832 AGCAGAGGTGGCAGCGAGGGA
1 AGCAGAGGT-ACAGCGAGAGA
29552853 AGCAGAGGCTACAGCGAGAGA
1 AGCAGAGG-TACAGCGAGAGA
*
29552874 AGTAGAGGT
1 AGCAGAGGT
29552883 TCAAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.45, T:0.08
Consensus pattern (20 bp):
AGCAGAGGTACAGCGAGAGA
Found at i:29553404 original size:85 final size:84
Alignment explanation
Indices: 29553315--29553478 Score: 240
Period size: 85 Copynumber: 1.9 Consensus size: 84
29553305 GTGAAGAAAG
* *
29553315 CGCCGCTAAAGAACATGATCTTTAGCGACATTTT-TCTCTAAGCGCCACTAAAGAACATGATCTT
1 CGCCGCTAAAGAACATGACCTTTAGCGAC-TTTTGTCTCTAAGCGCCACTAAAGAACATGACCTT
*
29553379 TAGCGGCGTCTTTTTTTTAAA
65 AAGCGGCGT-TTTTTTTTAAA
* * *
29553400 CGCCGCTAAAGAACATGACCTTTAGCGGCTTTTGTTTCTAAGCGCCGCTAAAGAACATGACCTTA
1 CGCCGCTAAAGAACATGACCTTTAGCGACTTTTGTCTCTAAGCGCCACTAAAGAACATGACCTTA
*
29553465 AGCGGTGTTTTTTT
66 AGCGGCGTTTTTTT
29553479 CTATAAATGC
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
84 10 0.14
85 61 0.86
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGACCTTTAGCGACTTTTGTCTCTAAGCGCCACTAAAGAACATGACCTTA
AGCGGCGTTTTTTTTTAAA
Found at i:29553423 original size:43 final size:42
Alignment explanation
Indices: 29553312--29553481 Score: 225
Period size: 42 Copynumber: 4.0 Consensus size: 42
29553302 TTTGTGAAGA
* * * *
29553312 AAGCGCCGCTAAAGAACATGATCTTTAGCGACATTTTTCTCT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCT
* * *
29553354 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGT-TTTTTTCT
*
29553397 AAACGCCGCTAAAGAACATGACCTTTAGCGGC-TTTTGTTTCT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT-TTTCT
* *
29553439 AAGCGCCGCTAAAGAACATGACCTTAAGCGGTGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCT
29553481 A
1 A
29553482 TAAATGCTGC
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.03
42 71 0.63
43 39 0.35
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCT
Found at i:29569750 original size:346 final size:351
Alignment explanation
Indices: 29569060--29569750 Score: 943
Period size: 346 Copynumber: 2.0 Consensus size: 351
29569050 TAGTAATCGG
* * *
29569060 CTGAGTAGCTAATGGGGTAGTTGTTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAATG
1 CTGAATAGCTAAAGGGGTAATTGTTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAATG
* * * *
29569125 AGTGAGTCCCATTCAAATTGTGACATGATTGAGTTTCTAGCAATTCGGTTTATACTCCACTGTGA
66 AG-GAGTCCCATTCAAATTGTGAAATAATTGAGTATCTAGCAATTCAGTTTATACTCCACTGTGA
* * *
29569190 TTGTTGAGTAAAAAATTCTTATGAAAAGTTGAGTCCCCTAATAAAAAATATAAAAAATAAATGTG
130 TTGTCGAGTAAAAAATTCATATGAAAAGTTGAATCCCCTAATAAAAAATATAAAAAATAAA---G
* * *
29569255 CATGTATTTGAGTATGTATAAGGCCAATAAAAAAGAGAGGAAAAAATGAAACTGGGTTTTGTTAA
192 -A-GTA-TT-AGTATGTATAAGGCCAATAAAAAAGAGAGAAAAAAATGAAACTAGGTTTAGTTAA
* * *
29569320 AAGATGAAATGGGTAAATTAGGAGATACTTGCTATAGTAGAAGTTTATGGATACTTACGATTTCT
253 AAGATGAAATAGGTAAATTAGGAGATACTTGCTATAGTAGAAGTGTATGGATACTTACGAGTTCT
29569385 TGTTTTTAGGGCAATATTTTCTAAATTGTCTTTC
318 TGTTTTTAGGGCAATATTTTCTAAATTGTCTTTC
* *
29569419 CTGAATAGCTAAAGGGTTAATTGTTTTA-TCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTCAT
1 CTGAATAGCTAAAGGGGTAATTG-TTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAAT
* * *
29569483 GA-GAGTCCCATTCAAATTGTGAAATAATTGAGTATCTGGCAATTCAGTTTATGCTCCATTGTGA
65 GAGGAGTCCCATTCAAATTGTGAAATAATTGAGTATCTAGCAATTCAGTTTATACTCCACTGTGA
* *
29569547 TTGTCGAGTCAAAAAA-TCATATGAAAAGTTGAATGCCCTAATAAAAAATATAATAAAT-AA-A-
130 TTGTCGAGT-AAAAAATTCATATGAAAAGTTGAATCCCCTAATAAAAAATATAAAAAATAAAGAG
*
29569608 TA-T-GTATGTATAAGGCCAGCA-AAAAAAGGGAGAAAAAAATGAAA-TCAGGTTTAGTTAAAAG
194 TATTAGTATGTATAAGGCCA--ATAAAAAAGAGAGAAAAAAATGAAACT-AGGTTTAGTTAAAAG
* * * *
29569669 ATGAACTAGGTAAATTAGGAGATACTTGCTATAGTGGAAGTGTATGGGTACTTAGGAGTTCTTGT
256 ATGAAATAGGTAAATTAGGAGATACTTGCTATAGTAGAAGTGTATGGATACTTACGAGTTCTTGT
29569734 TTTTAGGGCAATATTTT
321 TTTTAGGGCAATATTTT
29569751 TTGCACTGCC
Statistics
Matches: 299, Mismatches: 28, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
345 16 0.05
346 109 0.36
347 2 0.01
349 2 0.01
351 1 0.00
356 2 0.01
357 101 0.34
358 6 0.02
359 56 0.19
360 4 0.01
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (351 bp):
CTGAATAGCTAAAGGGGTAATTGTTTACTCCATCCATCTTTTTAGTCAAAAGCCTTAGCTTAATG
AGGAGTCCCATTCAAATTGTGAAATAATTGAGTATCTAGCAATTCAGTTTATACTCCACTGTGAT
TGTCGAGTAAAAAATTCATATGAAAAGTTGAATCCCCTAATAAAAAATATAAAAAATAAAGAGTA
TTAGTATGTATAAGGCCAATAAAAAAGAGAGAAAAAAATGAAACTAGGTTTAGTTAAAAGATGAA
ATAGGTAAATTAGGAGATACTTGCTATAGTAGAAGTGTATGGATACTTACGAGTTCTTGTTTTTA
GGGCAATATTTTCTAAATTGTCTTTC
Found at i:29595953 original size:6 final size:6
Alignment explanation
Indices: 29595936--29595965 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
29595926 TCAGATCTTG
29595936 TATTTAA TATTTA TATTTA TATTTA TATTT
1 TATTT-A TATTTA TATTTA TATTTA TATTT
29595966 GTTCGCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:29603844 original size:43 final size:43
Alignment explanation
Indices: 29603810--29603893 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
29603800 ATATACATGG
*
29603810 TTTGGCACACGACCGTGTGGCCCTATTTCTAATATACACACGA
1 TTTGGCACACGACCGTGTGGCCCTATTTCAAATATACACACGA
* *
29603853 TTTGGCACACGACCATGTGGCCCTATTTCAAATATTCACAC
1 TTTGGCACACGACCGTGTGGCCCTATTTCAAATATACACAC
29603894 AGGTGGACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (43 bp):
TTTGGCACACGACCGTGTGGCCCTATTTCAAATATACACACGA
Found at i:29603905 original size:43 final size:43
Alignment explanation
Indices: 29603812--29603906 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
29603802 ATACATGGTT
* * **
29603812 TGGCACACGACCGTGTGGCCCTATTTCTAATATACACACGATT
1 TGGCACACGACCATGTGGCCCTATTTCAAATATACACACGAGG
*
29603855 TGGCACACGACCATGTGGCCCTATTTCAAATATTCACAC-AGG
1 TGGCACACGACCATGTGGCCCTATTTCAAATATACACACGAGG
29603897 TGGACACACG
1 TGG-CACACG
29603907 GGCTGGGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 4 0.09
43 42 0.91
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (43 bp):
TGGCACACGACCATGTGGCCCTATTTCAAATATACACACGAGG
Found at i:29605949 original size:44 final size:43
Alignment explanation
Indices: 29605884--29606081 Score: 154
Period size: 44 Copynumber: 4.6 Consensus size: 43
29605874 TGATTTCATA
** *
29605884 TAAGACCATAGATGGGCTATGGCATCGATATATGAGACTTTC-TG
1 TAAGACCATATCTGGGATATGGCATCGATATATGAGA--TTCGTG
* * *
29605928 TAAGACCATATCTGGGATATGGCATTGGTATATGTGATTACGTG
1 TAAGACCATATCTGGGATATGGCATCGATATATGAGATT-CGTG
* * * **
29605972 TAAGACCATGTTTGGGACATTGGCATTAATATAT--GATTCGTG
1 TAAGACCATATCTGGGATA-TGGCATCGATATATGAGATTCGTG
* * * * *
29606014 TAAGACCAT-TGCTGGGCTATTGGCATCGATATGTGATAAT-ATG
1 TAAGACCATAT-CTGGGATA-TGGCATCGATATATGAGATTCGTG
*
29606057 TAAGACCATATCTGGGATTTGGCAT
1 TAAGACCATATCTGGGATATGGCAT
29606082 TGTATGTGAT
Statistics
Matches: 125, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.01
42 38 0.30
43 22 0.18
44 52 0.42
45 12 0.10
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (43 bp):
TAAGACCATATCTGGGATATGGCATCGATATATGAGATTCGTG
Found at i:29606036 original size:42 final size:44
Alignment explanation
Indices: 29605884--29606083 Score: 118
Period size: 42 Copynumber: 4.6 Consensus size: 44
29605874 TGATTTCATA
* * * *
29605884 TAAGACCATAGATGGGCTA-TGGCATCG-ATATATGAGACTTTC-TG
1 TAAGACCATTGCTGGGCTATTGGCATTGAATATAT--GA-TTACGTG
* * *
29605928 TAAGACCATAT-CTGGGATA-TGGCATTGGTATATGTGATTACGTG
1 TAAGACCAT-TGCTGGGCTATTGGCATT-GAATATATGATTACGTG
*
29605972 TAAGACCA-TGTTTGGGAC-ATTGGCATT-AATATATGATT-CGTG
1 TAAGACCATTG-CTGGG-CTATTGGCATTGAATATATGATTACGTG
* * * **
29606014 TAAGACCATTGCTGGGCTATTGGCATCG-ATATGTGATAATATG
1 TAAGACCATTGCTGGGCTATTGGCATTGAATATATGATTACGTG
*
29606057 TAAGACCATAT-CTGGGAT-TTGGCATTG
1 TAAGACCAT-TGCTGGGCTATTGGCATTG
29606084 TATGTGATAC
Statistics
Matches: 125, Mismatches: 18, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
41 1 0.01
42 41 0.33
43 31 0.25
44 39 0.31
45 8 0.06
46 5 0.04
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (44 bp):
TAAGACCATTGCTGGGCTATTGGCATTGAATATATGATTACGTG
Found at i:29606061 original size:85 final size:85
Alignment explanation
Indices: 29605926--29606082 Score: 194
Period size: 85 Copynumber: 1.8 Consensus size: 85
29605916 TGAGACTTTC
* * * * *
29605926 TGTAAGACCATATCTGGGATATGGCATTGGTATATGTGATTACGTGTAAGACCATGTTTGGGACA
1 TGTAAGACCATATCTGGGATATGGCATTCGTATATGTGATAACATGTAAGACCATATCTGGGA-A
29605991 TTGGCATTAATATATGATTCG
65 TTGGCATTAATATATGATTCG
* *
29606012 TGTAAGACCAT-TGCTGGGCTATTGGCA-TCG-ATATGTGATAATATGTAAGACCATATCTGGGA
1 TGTAAGACCATAT-CTGGGATA-TGGCATTCGTATATGTGATAACATGTAAGACCATATCTGGGA
*
29606074 TTTGGCATT
64 ATTGGCATT
29606083 GTATGTGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
84 8 0.13
85 28 0.46
86 20 0.33
87 5 0.08
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.34
Consensus pattern (85 bp):
TGTAAGACCATATCTGGGATATGGCATTCGTATATGTGATAACATGTAAGACCATATCTGGGAAT
TGGCATTAATATATGATTCG
Found at i:29606064 original size:43 final size:41
Alignment explanation
Indices: 29606012--29606092 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 41
29606002 ATATGATTCG
*
29606012 TGTAAGACCAT-TGCTGGGCTATTGGCATCGATATGTGATAATA
1 TGTAAGACCATAT-CTGGGAT-TTGGCATCG-TATGTGATAATA
*
29606055 TGTAAGACCATATCTGGGATTTGGCATTGTATGTGATA
1 TGTAAGACCATATCTGGGATTTGGCATCGTATGTGATA
29606093 CACGAGACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 9 0.26
42 8 0.23
43 17 0.49
44 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (41 bp):
TGTAAGACCATATCTGGGATTTGGCATCGTATGTGATAATA
Found at i:29606620 original size:15 final size:16
Alignment explanation
Indices: 29606600--29606637 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29606590 ACTTGATGCA
*
29606600 ATTATTT-GTAATGTG
1 ATTATTTAGTAATATG
29606615 ATTATTTAGTAATATG
1 ATTATTTAGTAATATG
29606631 AGTTATT
1 A-TTATT
29606638 ATATTACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (16 bp):
ATTATTTAGTAATATG
Found at i:29608626 original size:12 final size:12
Alignment explanation
Indices: 29608609--29608639 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
29608599 GAATTTGAAT
29608609 GGAGTTGTTGAG
1 GGAGTTGTTGAG
29608621 GGAGTTGTTGAG
1 GGAGTTGTTGAG
29608633 GGAGTTG
1 GGAGTTG
29608640 AGGAGGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (12 bp):
GGAGTTGTTGAG
Found at i:29609894 original size:27 final size:26
Alignment explanation
Indices: 29609841--29609897 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
29609831 CAATATCTGC
*
29609841 ACCGAAATACCCCACAAGATAACATG
1 ACCGAAATACCCCACAAGATAAAATG
*
29609867 ACCGAAATACCCC-CATAGGGTAAAATG
1 ACCGAAATACCCCACA-A-GATAAAATG
29609894 ACCG
1 ACCG
29609898 TGTAATAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.52
27 11 0.41
ACGTcount: A:0.42, C:0.30, G:0.16, T:0.12
Consensus pattern (26 bp):
ACCGAAATACCCCACAAGATAAAATG
Found at i:29612708 original size:27 final size:26
Alignment explanation
Indices: 29612665--29612773 Score: 137
Period size: 27 Copynumber: 4.1 Consensus size: 26
29612655 GGATGTTACA
** *
29612665 GACCGAAATACTTCATAGGATAAAAT
1 GACCGAAATACCCCATAGGGTAAAAT
*
29612691 GACCAAAATACCCCCATAGGGTAAAAT
1 GACCGAAATA-CCCCATAGGGTAAAAT
* *
29612718 AATCGAAATACCCCATAGGGTAAAAT
1 GACCGAAATACCCCATAGGGTAAAAT
*
29612744 GACTGAAATATCCCCATAGGGTAAAAT
1 GACCGAAATA-CCCCATAGGGTAAAAT
29612771 GAC
1 GAC
29612774 TGTTATACCC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
26 32 0.45
27 39 0.55
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (26 bp):
GACCGAAATACCCCATAGGGTAAAAT
Found at i:29612774 original size:27 final size:26
Alignment explanation
Indices: 29612669--29612802 Score: 128
Period size: 27 Copynumber: 5.0 Consensus size: 26
29612659 GTTACAGACC
** * *
29612669 GAAATACTTCATAGGATAAAATGACC
1 GAAATACCCCATAGGGTAAAATGACT
* *
29612695 AAAATACCCCCATAGGGTAAAAT-AAT
1 GAAATA-CCCCATAGGGTAAAATGACT
29612721 CGAAATACCCCATAGGGTAAAATGACT
1 -GAAATACCCCATAGGGTAAAATGACT
29612748 GAAATATCCCCATAGGGTAAAATGACT
1 GAAATA-CCCCATAGGGTAAAATGACT
** *
29612775 GTTATACCCC-TAGGAGATGAAATGACT
1 GAAATACCCCATAGG-G-TAAAATGACT
29612802 G
1 G
29612803 TTATGGCCAT
Statistics
Matches: 91, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.04
26 33 0.36
27 54 0.59
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (26 bp):
GAAATACCCCATAGGGTAAAATGACT
Found at i:29612784 original size:53 final size:53
Alignment explanation
Indices: 29612668--29612770 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
29612658 TGTTACAGAC
** * **
29612668 CGAAATACTTCATAGGATAAAATGACCAAAATACCCCCATAGGGTAAAATAAT
1 CGAAATACCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAATAAT
*
29612721 CGAAATACCCCATAGGGTAAAATGACTGAAATATCCCCATAGGGTAAAAT
1 CGAAATACCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAAT
29612771 GACTGTTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (53 bp):
CGAAATACCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAATAAT
Found at i:29616091 original size:4 final size:4
Alignment explanation
Indices: 29616082--29616106 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29616072 TCAATTATTC
29616082 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
29616107 ACAAGAGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:29616629 original size:21 final size:21
Alignment explanation
Indices: 29616604--29616643 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29616594 CCATCACTCA
29616604 TTTTAACCAT-TTATTAATATT
1 TTTTAACCATATT-TTAATATT
*
29616625 TTTTAATCATATTTTAATA
1 TTTTAACCATATTTTAATA
29616644 CCGTGTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAACCATATTTTAATATT
Found at i:29616974 original size:44 final size:43
Alignment explanation
Indices: 29616926--29617018 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 43
29616916 TAGTTAAAAA
* *
29616926 TAAAATATAATAGAAGTTGCCATAATTATACATTTAAAAATGAT
1 TAAAATATAATAGAAGTTGCCATAATTATACAATT-AAAATAAT
* ** ** *
29616970 TAAAATTTAATAGATTTTGTGATAATTATATAATTAAAATAAT
1 TAAAATATAATAGAAGTTGCCATAATTATACAATTAAAATAAT
29617013 TAAAAT
1 TAAAAT
29617019 TAAAATTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 13 0.32
44 28 0.68
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.39
Consensus pattern (43 bp):
TAAAATATAATAGAAGTTGCCATAATTATACAATTAAAATAAT
Found at i:29617021 original size:15 final size:16
Alignment explanation
Indices: 29616991--29617031 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
29616981 AGATTTTGTG
29616991 ATAATTATATAATTAAA
1 ATAATTA-ATAATTAAA
29617008 ATAATTAA-AATTAAA
1 ATAATTAATAATTAAA
*
29617023 ATTATTAAT
1 ATAATTAAT
29617032 TAAAAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATTAATAATTAAA
Found at i:29625550 original size:20 final size:21
Alignment explanation
Indices: 29625521--29625572 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
29625511 TTAGGAAGAA
*
29625521 TTAAATTTTTTTA-TATGTTCT
1 TTAAA-TTTTTTAGAATGTTCT
*
29625542 TTAAATTTTTTAGAATTTTCT
1 TTAAATTTTTTAGAATGTTCT
*
29625563 TTTAATTTTT
1 TTAAATTTTT
29625573 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTAAATTTTTTAGAATGTTCT
Found at i:29625573 original size:20 final size:21
Alignment explanation
Indices: 29625521--29625586 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
29625511 TTAGGAAGAA
* *
29625521 TTAAATTTTTTTA-TATGTTCT
1 TTAAA-TTTTTTAGAATTTTCT
29625542 TTAAATTTTTTAGAATTTTCT
1 TTAAATTTTTTAGAATTTTCT
* *
29625563 TTTAA-TTTTTATAATTTT-T
1 TTAAATTTTTTAGAATTTTCT
29625582 TTAAA
1 TTAAA
29625587 ATATAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 5 0.13
20 19 0.49
21 15 0.38
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTAAATTTTTTAGAATTTTCT
Found at i:29630967 original size:14 final size:14
Alignment explanation
Indices: 29630948--29630987 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29630938 TTGATTGGCA
29630948 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
29630962 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
29630976 GGAAAATGTTTT
1 GTAAAATGTTTT
29630988 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:29630996 original size:20 final size:20
Alignment explanation
Indices: 29630971--29631010 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29630961 CGTAAAATGA
*
29630971 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
29630991 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
29631011 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:29631000 original size:34 final size:35
Alignment explanation
Indices: 29630956--29631022 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
29630946 CAGTAAAATG
*
29630956 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
29630990 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
29631023 CTAGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:29631134 original size:20 final size:20
Alignment explanation
Indices: 29631109--29631147 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29631099 GTTTTTACAT
29631109 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
29631129 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
29631148 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:29631207 original size:15 final size:15
Alignment explanation
Indices: 29631178--29631230 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
29631168 TATTGCAATG
*
29631178 ATTTATTTATAAATAA
1 ATTT-TTTATTAATAA
29631194 ATTTTTTATTAATAAA
1 ATTTTTTATTAAT-AA
29631210 AGTTTTTTATCTAATTAA
1 A-TTTTTTAT-TAA-TAA
29631228 ATT
1 ATT
29631231 CCAAATGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 10 0.31
18 6 0.19
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTTTTATTAATAA
Found at i:29631421 original size:14 final size:14
Alignment explanation
Indices: 29631402--29631441 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29631392 TTGATTGCCA
29631402 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
29631416 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
29631430 GGAAAATGTTTT
1 GTAAAATGTTTT
29631442 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:29634281 original size:18 final size:18
Alignment explanation
Indices: 29634260--29634310 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
29634250 AGGAATGAAG
29634260 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** *
29634278 GAAGGGAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
29634296 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
29634311 CCTGAGAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:29634944 original size:42 final size:42
Alignment explanation
Indices: 29634876--29634999 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
29634866 ACTGAGATGT
* * *
29634876 GATTTGTGTAAGACCATGTCTAGGACATTGGCATCGATATGA
1 GATTCGTGTAAGACCATGTCTAGGACATTAGCACCGATATGA
* *
29634918 GATTCGTGTAAGACCATGTTTGGGACATTAGCACCGATATGA
1 GATTCGTGTAAGACCATGTCTAGGACATTAGCACCGATATGA
*
29634960 GATTCGTGTAAGACCATAG-CTAGG-CTATTAGCATCGATAT
1 GATTCGTGTAAGACCAT-GTCTAGGAC-ATTAGCACCGATAT
29635000 ATGATAGTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 70 0.97
43 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
GATTCGTGTAAGACCATGTCTAGGACATTAGCACCGATATGA
Found at i:29637929 original size:2 final size:2
Alignment explanation
Indices: 29637922--29637955 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
29637912 ATATAGGCAT
*
29637922 CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29637956 TATATATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:29640468 original size:11 final size:11
Alignment explanation
Indices: 29640446--29640503 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
29640436 AATTAATCCT
29640446 CTCTCAAATTTC
1 CTCTC-AATTTC
29640458 CTCTCAATTTC
1 CTCTCAATTTC
*
29640469 CTCTAAATTTC
1 CTCTCAATTTC
*
29640480 CTCTCAATTTG
1 CTCTCAATTTC
*
29640491 CTCTCAAATTC
1 CTCTCAATTTC
29640502 CT
1 CT
29640504 TCCAAATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:29640479 original size:22 final size:23
Alignment explanation
Indices: 29640446--29640521 Score: 97
Period size: 22 Copynumber: 3.4 Consensus size: 23
29640436 AATTAATCCT
29640446 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
29640469 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
29640491 CTCTCAAA-TTCCT-TCCAAATTT-
1 CTCTCAAATTTCCTCT-C-AATTTC
29640513 CTCTCAAAT
1 CTCTCAAAT
29640522 CCATATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 1 0.02
22 35 0.73
23 12 0.25
ACGTcount: A:0.25, C:0.32, G:0.01, T:0.42
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:29640495 original size:33 final size:33
Alignment explanation
Indices: 29640445--29640519 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
29640435 AAATTAATCC
* *
29640445 TCTCTCAAATTTCCTCTCAATTTCC-TCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCCAAATT
*
29640478 TCCTCTCAATTTGCTCTCAAATTCCTTCCAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCCAAATT
29640512 TCTCTCAA
1 TCTCTCAA
29640520 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.24, C:0.32, G:0.01, T:0.43
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCCAAATT
Found at i:29640520 original size:11 final size:11
Alignment explanation
Indices: 29640445--29640521 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
29640435 AAATTAATCC
29640445 TCTCTCAAATT
1 TCTCTCAAATT
29640456 TCCTCTC-AATT
1 T-CTCTCAAATT
29640467 TC-CTCTAAATT
1 TCTCTC-AAATT
29640478 TCCTCTC-AATT
1 T-CTCTCAAATT
29640489 TGCTCTCAAATT
1 T-CTCTCAAATT
*
29640501 CCT-TCCAAATT
1 TCTCT-CAAATT
29640512 TCTCTCAAAT
1 TCTCTCAAAT
29640522 CCATATTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 3 0.05
10 2 0.04
11 36 0.65
12 11 0.20
13 3 0.05
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:29641642 original size:7 final size:7
Alignment explanation
Indices: 29641630--29641655 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29641620 TAGTCGATTG
29641630 GTATTTA
1 GTATTTA
29641637 GTATTTA
1 GTATTTA
29641644 GTATTTA
1 GTATTTA
29641651 GTATT
1 GTATT
29641656 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:29642837 original size:25 final size:25
Alignment explanation
Indices: 29642801--29642883 Score: 121
Period size: 25 Copynumber: 3.3 Consensus size: 25
29642791 TATTTTGATA
* * *
29642801 TTATTTGTTGTAATAAAATGGACGT
1 TTATTTGATGTAATAAAATAGAAGT
29642826 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
29642851 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
*
29642876 TTTTTTGA
1 TTATTTGA
29642884 GTTATTTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:29642953 original size:95 final size:95
Alignment explanation
Indices: 29642745--29642954 Score: 209
Period size: 95 Copynumber: 2.2 Consensus size: 95
29642735 AAATATTTTG
* *
29642745 AATATTTTGATATTATTTT-ATGTAATAAAATAAAAAAATTTTGAGTTATTTTGATATTATTTGT
1 AATATTTTGA-AGTATTTTGATGTAATAAAATAAAAAAATTTTGAGTTATTTTGATATTATTTGA
* * *
29642809 TGTAATAAAATGGACGTTTATTTGATGTAAT
65 TGTAATAAAATGGACGATTAATTAATGTAAT
* * * ***
29642840 AA-A-ATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTG
1 AATATTTTGAAGTAT-TTTGATGTAATAAAATA-AAAAAATTTTGAGTTATTTTGATATTATTTG
*
29642903 ATGTAATAACAT-GA-GATTAATTAATTTGTACA-
64 ATGTAATAAAATGGACGATTAATTAA--TGTA-AT
29642935 AATATTTTGAA-TATTTTGAT
1 AATATTTTGAAGTATTTTGAT
29642955 ATTATTTGAG
Statistics
Matches: 92, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
92 3 0.03
93 13 0.14
94 16 0.17
95 52 0.57
96 4 0.04
97 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (95 bp):
AATATTTTGAAGTATTTTGATGTAATAAAATAAAAAAATTTTGAGTTATTTTGATATTATTTGAT
GTAATAAAATGGACGATTAATTAATGTAAT
Found at i:29646317 original size:124 final size:124
Alignment explanation
Indices: 29646072--29646443 Score: 577
Period size: 124 Copynumber: 3.0 Consensus size: 124
29646062 CAAACATGCT
29646072 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
*
29646137 GAAGGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
66 GAAGCATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
* * * *
29646196 ACTGTAGCAAAAGTGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGGT
* * * **
29646260 TGAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTTC-AGGACTT
65 AGAAGCA-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
*
29646320 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
* * *
29646385 AAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTATAGGACC
66 GAAGC-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACC
29646444 TAAAAACCCT
Statistics
Matches: 221, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
123 2 0.01
124 168 0.76
125 51 0.23
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
GAAGCATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACCA
Found at i:29651099 original size:34 final size:34
Alignment explanation
Indices: 29651045--29651109 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
29651035 CCGAATATAA
29651045 TAAATATATTTTTTTATTTTTAT-TTTTTAATTT
1 TAAATATATTTTTTTATTTTTATATTTTTAATTT
*
29651078 TAAA-ATACTTTTTTTATTTTTTTTATTTTTAA
1 TAAATATA-TTTTTTTA-TTTTTATATTTTTAA
29651110 AATGATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 3 0.11
33 12 0.43
34 6 0.21
35 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (34 bp):
TAAATATATTTTTTTATTTTTATATTTTTAATTT
Found at i:29651105 original size:28 final size:28
Alignment explanation
Indices: 29651061--29651120 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
29651051 TATTTTTTTA
29651061 TTTTTATTTTTTAA-TTTTAAAAT-ACTT
1 TTTTTATTTTTTAATTTTTAAAATGA-TT
*
29651088 TTTTTATTTTTTTTATTTTTAAAATGATT
1 TTTTTA-TTTTTTAATTTTTAAAATGATT
29651117 TTTT
1 TTTT
29651121 AATGTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.21
28 7 0.24
29 15 0.52
30 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (28 bp):
TTTTTATTTTTTAATTTTTAAAATGATT
Found at i:29651981 original size:19 final size:21
Alignment explanation
Indices: 29651957--29652001 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29651947 ACATCATTTC
*
29651957 CAGAAGC-CCGAAG-GCTAAA
1 CAGAAGCACAGAAGTGCTAAA
*
29651976 CAGAAGCACATAAGTGCTAAA
1 CAGAAGCACAGAAGTGCTAAA
29651997 CAGAA
1 CAGAA
29652002 ACCCATAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (21 bp):
CAGAAGCACAGAAGTGCTAAA
Found at i:29652021 original size:42 final size:42
Alignment explanation
Indices: 29651972--29652127 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 42
29651962 GCCCGAAGGC
* *
29651972 TAAACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* ** * *
29652014 TGAACAGAAGCTTGTAAGAGCTGAACAAAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
29652056 TAAACAGAAACTCAAAAGAACTAAACGGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
29652098 TAAACATAAACTCATATGAGTTAAACAGAA
1 TAAACAGAAGCTCATAAGAGCTAAACAGAA
29652128 GCTCGTGAGA
Statistics
Matches: 92, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.49, C:0.17, G:0.18, T:0.16
Consensus pattern (42 bp):
TAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:29652061 original size:21 final size:21
Alignment explanation
Indices: 29651972--29652127 Score: 105
Period size: 21 Copynumber: 7.4 Consensus size: 21
29651962 GCCCGAAGGC
* * * *
29651972 TAAACAGAAGCACATAAGTGC
1 TAAACAGAAACCCATAAGAGT
*
29651993 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGAGT
* * *** *
29652014 TGAACAGAAGCTTGTAAGAGC
1 TAAACAGAAACCCATAAGAGT
* * *
29652035 TGAACAAAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGAGT
* * **
29652056 TAAACAGAAACTCAAAAGAAC
1 TAAACAGAAACCCATAAGAGT
* *
29652077 TAAACGGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGAGT
* * *
29652098 TAAACATAAACTCATATGAGT
1 TAAACAGAAACCCATAAGAGT
29652119 TAAACAGAA
1 TAAACAGAA
29652128 GCTCGTGAGA
Statistics
Matches: 98, Mismatches: 37, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 98 1.00
ACGTcount: A:0.49, C:0.17, G:0.18, T:0.16
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGAGT
Found at i:29653755 original size:19 final size:19
Alignment explanation
Indices: 29653727--29653773 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
29653717 GGCATAGTTA
29653727 TAAAAA-ATATGTATATAT
1 TAAAAATATATGTATATAT
29653745 TAAAAATATATGTATATAT
1 TAAAAATATATGTATATAT
29653764 TAAAAATATA
1 TAAAAATATA
29653774 CGTAAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
TAAAAATATATGTATATAT
Found at i:29663426 original size:21 final size:21
Alignment explanation
Indices: 29663385--29663426 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29663375 AAAATTTTAG
* *
29663385 AAATTTCTAAAATATATAAAT
1 AAATTTCAAAAATATAAAAAT
29663406 AAATATTCAAAAATA-AAAAAT
1 AAAT-TTCAAAAATATAAAAAT
29663427 TAGTTAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTTCAAAAATATAAAAAT
Found at i:29663514 original size:29 final size:30
Alignment explanation
Indices: 29663474--29663530 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
29663464 GAAAATTATG
*
29663474 AAATATATAAATAT-ATAAACTAAAAATAA
1 AAATATATAAATATAATAAACAAAAAATAA
*
29663503 AAATCATA-AAATTTAATAAACAAAAAAT
1 AAAT-ATATAAATATAATAAACAAAAAAT
29663531 TAAACATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (30 bp):
AAATATATAAATATAATAAACAAAAAATAA
Found at i:29664993 original size:11 final size:11
Alignment explanation
Indices: 29664959--29665002 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
29664949 ATTTTAAAAA
*
29664959 TAAAAATTTTT
1 TAAAAATATTT
29664970 TACAAAAAGTATTT
1 T--AAAAA-TATTT
29664984 TAAAAATATTT
1 TAAAAATATTT
29664995 TAAAAATA
1 TAAAAATA
29665003 AAAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 14 0.48
12 5 0.17
13 5 0.17
14 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:29667967 original size:7 final size:7
Alignment explanation
Indices: 29667955--29667985 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
29667945 AATGAATTGG
29667955 AAAATGT
1 AAAATGT
29667962 AAAATGT
1 AAAATGT
29667969 AAAATGT
1 AAAATGT
29667976 AAAATGT
1 AAAATGT
29667983 AAA
1 AAA
29667986 TTTTTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (7 bp):
AAAATGT
Found at i:29668523 original size:81 final size:77
Alignment explanation
Indices: 29668359--29668523 Score: 183
Period size: 82 Copynumber: 2.1 Consensus size: 77
29668349 TAGAAGTTCC
* *
29668359 ATTTTTAAGTTGTGAGTTACTAAAGAAAATAAAAGTTGACAGACACAAAAAAACTCCTTGATTGA
1 ATTTTTAAGTTGTGAGTTACTAAAAAAAAAAAAAGTTGACAGACACAAAAAAACTCCTTGATTGA
*
29668424 AGACTAGAAGTGCC
66 AGAC-A-AAGTGCA
*
29668438 ATTTTTAAGTTGTGCGAGTTACTAAAAAAAAAAAGAAAGTTGA-AGGACAC-AAAAAACTTCTTG
1 ATTTTTAAGTTGT--GAGTTACT-AAAAAAAAAA-AAAGTTGACA-GACACAAAAAAACTCCTTG
*
29668501 ATTGATGAGC-AAGTAGCA
61 ATTGAAGA-CAAAGT-GCA
29668519 ATTTT
1 ATTTT
29668524 CCTTTTCACA
Statistics
Matches: 74, Mismatches: 5, Indels: 12
0.81 0.05 0.13
Matches are distributed among these distances:
79 13 0.18
80 4 0.05
81 15 0.20
82 28 0.38
83 14 0.19
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (77 bp):
ATTTTTAAGTTGTGAGTTACTAAAAAAAAAAAAAGTTGACAGACACAAAAAAACTCCTTGATTGA
AGACAAAGTGCA
Found at i:29678432 original size:45 final size:45
Alignment explanation
Indices: 29678379--29678469 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
29678369 AAATAAATGA
29678379 ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
1 ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
*
29678424 ATTTCAAGTTGCTATAACATATGGATTTTGACATATAAACTAAAG
1 ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
29678469 A
1 A
29678470 AATTATATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (45 bp):
ATTTCAAGTTGCTATAACATATGGATTATGACATATAAACTAAAG
Found at i:29678450 original size:24 final size:24
Alignment explanation
Indices: 29678379--29678451 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
29678369 AAATAAATGA
29678379 ATTTCAAGTTGCTATAACATATGG
1 ATTTCAAGTTGCTATAACATATGG
**
29678403 A-TT--A--TGACATATAA-ACTAAAG
1 ATTTCAAGTTG-C-TATAACA-TATGG
29678424 ATTTCAAGTTGCTATAACATATGG
1 ATTTCAAGTTGCTATAACATATGG
29678448 ATTT
1 ATTT
29678452 TGACATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 10 0.28
22 2 0.06
23 2 0.06
24 14 0.39
25 2 0.06
26 2 0.06
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (24 bp):
ATTTCAAGTTGCTATAACATATGG
Found at i:29678649 original size:11 final size:11
Alignment explanation
Indices: 29678633--29678664 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
29678623 ATAAAGTAGA
29678633 TTATATATTAT
1 TTATATATTAT
29678644 TTATATATTA-
1 TTATATATTAT
29678654 TTATATATTAT
1 TTATATATTAT
29678665 GATTTTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATATATTAT
Found at i:29678727 original size:18 final size:18
Alignment explanation
Indices: 29678704--29678739 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29678694 ATATTAAGAA
29678704 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
29678722 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
29678740 AATAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTAAATTATATTT
Found at i:29678991 original size:16 final size:16
Alignment explanation
Indices: 29678970--29679005 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29678960 CTGAATTACT
* *
29678970 ATTACAGCTCTATTTC
1 ATTACACCTCTATTCC
29678986 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
29679002 ATTA
1 ATTA
29679006 TAGTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:29679396 original size:9 final size:9
Alignment explanation
Indices: 29679382--29679412 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29679372 GTTAAACGAA
29679382 TCGAGTTAT
1 TCGAGTTAT
*
29679391 TCGAGTTAA
1 TCGAGTTAT
29679400 TCGAGTTAT
1 TCGAGTTAT
29679409 TCGA
1 TCGA
29679413 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29679486 original size:18 final size:18
Alignment explanation
Indices: 29679465--29679501 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29679455 TGAGTTTTCG
*
29679465 AATTCGAATAACTCGAAT
1 AATTCAAATAACTCGAAT
*
29679483 AATTCAAATAAGTCGAAT
1 AATTCAAATAACTCGAAT
29679501 A
1 A
29679502 TCAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTCAAATAACTCGAAT
Found at i:29679749 original size:30 final size:31
Alignment explanation
Indices: 29679715--29679774 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
29679705 AAACATTTTA
*
29679715 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
29679745 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
29679775 TCTCAGCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:29681552 original size:21 final size:21
Alignment explanation
Indices: 29681528--29681567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29681518 TTTAAAATTA
29681528 GATTGTTTTCTA-AATTTTAAG
1 GATT-TTTTCTAGAATTTTAAG
*
29681549 GATTTTTTTTAGAATTTTA
1 GATTTTTTCTAGAATTTTA
29681568 GATATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (21 bp):
GATTTTTTCTAGAATTTTAAG
Found at i:29683074 original size:12 final size:12
Alignment explanation
Indices: 29683057--29683089 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
29683047 ATTTTAACAC
29683057 TATTATTATCAT
1 TATTATTATCAT
29683069 TATTATTATCAT
1 TATTATTATCAT
29683081 TATTATTAT
1 TATTATTAT
29683090 ACTTACGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATCAT
Found at i:29683258 original size:27 final size:26
Alignment explanation
Indices: 29683204--29683305 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 26
29683194 TTTTCGTAGT
29683204 TTTTATATATATGTATATACATTTATA
1 TTTTATA-ATATGTATATACATTTATA
29683231 TTTTATAATAT-T-TATACATTTTCCATA
1 TTTTATAATATGTATATACA-TTT--ATA
* * * **
29683258 TTATATAATCTATATATATGTTTATACA
1 TTTTATAATATGTATATACATTTAT--A
29683286 TTTTTTATAATATGTATATA
1 --TTTTATAATATGTATATA
29683306 TATACATATA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
24 6 0.10
25 4 0.07
26 6 0.10
27 19 0.32
28 5 0.08
29 4 0.07
30 15 0.25
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTTATAATATGTATATACATTTATA
Found at i:29683378 original size:24 final size:24
Alignment explanation
Indices: 29683347--29683421 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 24
29683337 TTTCATAGTT
*
29683347 TTTATATATTTATATATGTATATACA
1 TTTATAT-TTTATA-ATATATATACA
*
29683373 TTTATATTTTATAATATCTATACA
1 TTTATATTTTATAATATATATACA
*
29683397 TTTTCCATATTTTATAATCTATATA
1 -TTT--ATATTTTATAATATATATA
29683422 TATATGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.21
25 9 0.21
26 7 0.17
27 17 0.40
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.55
Consensus pattern (24 bp):
TTTATATTTTATAATATATATACA
Found at i:29683395 original size:148 final size:143
Alignment explanation
Indices: 29683181--29683458 Score: 450
Period size: 148 Copynumber: 1.9 Consensus size: 143
29683171 ATTATTATCA
* *
29683181 TATTATTATTTTATTTTCGTAGTTTTTATATATATGTATATACATTTATATTTTATAATATTTAT
1 TATTATTATTTTATTTTCATAGTTTTTATATATATGTATATACATTTATATTTTATAATATCTAT
*
29683246 ACATTTTCCATATTATATAATC-TATATATATGTTTATACATTTTTTATAATATGTATATATATA
66 ACATTTTCCATATTATATAATCATATATATATGTTTATACATTCTTTATAATATGTATATATATA
29683310 CATATACATCTTT
131 CATATACATCTTT
29683323 TATTATTATTTTATTTTCATAGTTTTTATATATTTATATATGTATATACATTTATATTTTATAAT
1 TATTATTATTTTATTTTCATAG--TTT-T-TA--TATATATGTATATACATTTATATTTTATAAT
*
29683388 ATCTATACATTTTCCATATTTTATAATCTATATATATATGTTTATACATTCTTTATAATATGTAT
60 ATCTATACATTTTCCATATTATATAATC-ATATATATATGTTTATACATTCTTTATAATATGTAT
29683453 ATATAT
124 ATATAT
29683459 TTTCTTACAC
Statistics
Matches: 124, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
142 21 0.17
144 3 0.02
145 1 0.01
146 2 0.02
148 57 0.46
150 40 0.32
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (143 bp):
TATTATTATTTTATTTTCATAGTTTTTATATATATGTATATACATTTATATTTTATAATATCTAT
ACATTTTCCATATTATATAATCATATATATATGTTTATACATTCTTTATAATATGTATATATATA
CATATACATCTTT
Found at i:29683511 original size:148 final size:148
Alignment explanation
Indices: 29683209--29683511 Score: 375
Period size: 148 Copynumber: 2.0 Consensus size: 148
29683199 GTAGTTTTTA
*
29683209 TATATATGTATATACATTTATATTTTATAATATTTATACATTTTCCATATTATATAATCTATATA
1 TATATATGTATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
* * ** * * **
29683274 TATGTTTATACATTTTTTATAATATGTATATATATACATATACATCTTTTATTATTATTTTATTT
66 TATGTTTATACATTCTTTATAATATGTATATATATACATATACATCTTTCAAAACTATTATATAA
* *
29683339 TCATAGTTTTTATATATT
131 TCATAGTTTTCACATATT
*
29683357 TATATATGTATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAATCTATATA
1 TATATATGTATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATC--TATA
*
29683422 TATATGTTTATACATTCTTTATAATATGTATATATATTTTC-T-TACA-CTATTCAAAACTATTA
64 TATATGTTTATACATTCTTTATAATATGTATATATA--TACATATACATCT-TTCAAAACTATTA
*
29683484 TA-AAT-ATA-TTTTCCACATTTT
126 TATAATCATAGTTTT-CACATATT
*
29683505 TTTATAT
1 TATATAT
29683512 ATACATATAT
Statistics
Matches: 134, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
147 4 0.03
148 71 0.53
149 3 0.02
150 53 0.40
151 1 0.01
152 2 0.01
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (148 bp):
TATATATGTATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATA
TATGTTTATACATTCTTTATAATATGTATATATATACATATACATCTTTCAAAACTATTATATAA
TCATAGTTTTCACATATT
Found at i:29685283 original size:16 final size:16
Alignment explanation
Indices: 29685258--29685288 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29685248 TGTGTTTTGT
*
29685258 TTTGATTGCATGACAC
1 TTTGACTGCATGACAC
29685274 TTTGACTGCATGACA
1 TTTGACTGCATGACA
29685289 TTTCATTATA
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:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (16 bp):
TTTGACTGCATGACAC
Found at i:29690081 original size:41 final size:40
Alignment explanation
Indices: 29689981--29690514 Score: 210
Period size: 41 Copynumber: 12.7 Consensus size: 40
29689971 AAACCGGTGA
* * ** * * *
29689981 AATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
1 AATCAGTCTTATCTCCCTGAAGTTGCAGAAGAGC-AAATAG
* *
29690022 AATCAGATCTTATCTCTCTGAAGTTGCAGAAGAGCAAATCG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGAAGAGCAAATAG
* * ** * * *
29690063 CATCCAGTCTTATCTCTCTGAAGTTGCAGTGGAGCGGATTAA
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGAAGAGC-AAATAG
* * *
29690105 AATCAGATCTTATCTCTCTGAAGTTGCA-ATAGAGCAGATCG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGA-AGAGCAAATAG
* * ** *
29690146 CATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAG
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGAAGAGCA-A-A-TAG
* * * ** * * *
29690190 AAATCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAA
1 -AATCAGTCTTATCTCCCTGAAGTTGCAGAAGAGC-AAATAG
** * *
29690232 AATCAGATCTTATCTCTTTGAAGTTGCAGAAGAGCAGATCG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGAAGAGCAAATAG
* *
29690273 CATCCAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAGA-AG
1 AAT-CAGTCTTATCTCCCTGAAGTTGCA--GAAG-AG-CAAATAG
* * * * * *
29690317 AAATCAATCCTATCTCCCTGAAGTTGCAG-TGAAGCGGATTAA
1 -AATCAGTCTTATCTCCCTGAAGTTGCAGAAG-AGC-AAATAG
* * * *
29690359 AATCAGATCTTATCTCTCTGAAGTTGCAGAAGAGTAGATTG
1 AATCAG-TCTTATCTCCCTGAAGTTGCAGAAGAGCAAATAG
* * * ** ** * *
29690400 CATCCAGTCCTATCTCCCTGAGGTTGCAGTGGAGTGGATTAAA
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAGAAGAG-CAAAT-AG
** ** * *
29690443 AATTACAGATCTTATCTCTTTGAAGTTGCATTAGAGCAGATCG
1 AA-T-CAG-TCTTATCTCCCTGAAGTTGCAGAAGAGCAAATAG
*
29690486 CATCCAGTCTTATCTCCCTGAAGTTGCAG
1 AAT-CAGTCTTATCTCCCTGAAGTTGCAG
29690515 TGGAGTAGAC
Statistics
Matches: 360, Mismatches: 105, Indels: 56
0.69 0.20 0.11
Matches are distributed among these distances:
40 1 0.00
41 145 0.40
42 116 0.32
43 8 0.02
44 61 0.17
45 29 0.08
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (40 bp):
AATCAGTCTTATCTCCCTGAAGTTGCAGAAGAGCAAATAG
Found at i:29690129 original size:83 final size:83
Alignment explanation
Indices: 29689990--29690519 Score: 509
Period size: 83 Copynumber: 6.3 Consensus size: 83
29689980 AAATCAATCC
29689990 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
29690055 GCAAATCGCATCCAGTCT
66 GCAAATCGCATCCAGTCT
*
29690073 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCA-ATAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGA-AG
* *
29690137 AGCAGATCGCATCCAATCT
65 AGCAAATCGCATCCAGTCT
* ** * * * *
29690156 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCA-ATCCTATCTCCCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGC-G-GATTA-AAATCAGATCTTATCTCTCTGAAGTTGCAGA
* * * ***
29690220 GGAGCGGATTAAAAT-CAGATCT
63 AGAGC-AAATCGCATCCAG-TCT
** ** * *** *
29690242 TATCTCTTTGAAGTTGCAGAAGAGCAGA-TCGCATCCAG-TCTTATCTCCCTGAAGTTGCAGTGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAT-CAGATCTTATCTCTCTGAAGTTGCA--GA
* * *
29690305 AGCAGACAGAA--GAAAT-CAATCC
63 AG-AG-CA-AATCG-CATCCAGTCT
*
29690327 TATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
* * * *
29690392 GTAGATTGCATCCAGTCC
66 GCAAATCGCATCCAGTCT
* * * **
29690410 TATCTCCCTGAGGTTGCAGTGGAGTGGATTAAAAATTACAGATCTTATCTCTTTGAAGTTGCATT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAA-T-CAGATCTTATCTCTCTGAAGTTGCAGA
*
29690475 AGAGCAGATCGCATCCAGTCT
63 AGAGCAAATCGCATCCAGTCT
29690496 TATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
29690520 TAGACTAGAG
Statistics
Matches: 362, Mismatches: 62, Indels: 43
0.78 0.13 0.09
Matches are distributed among these distances:
81 1 0.00
82 6 0.02
83 158 0.44
84 10 0.03
85 57 0.16
86 128 0.35
87 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (83 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
GCAAATCGCATCCAGTCT
Found at i:29690214 original size:44 final size:43
Alignment explanation
Indices: 29689979--29690387 Score: 248
Period size: 42 Copynumber: 9.7 Consensus size: 43
29689969 ATAAACCGGT
* * * **
29689979 GAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GGATTA
1 GAAATCAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGAA
*
29690021 -AAATCAGATCTTATCTCTCTGAAGTTGCA--GAAG-AGCA-AA
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGAA
* * * * * **
29690060 TCG-CATCCAGTCTTATCTCTCTGAAGTTGCAGTGGAGC-GGATTA
1 --GAAAT-CAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGAA
* * *
29690104 -AAATCAGATCTTATCTCTCTGAAGTTGCAAT--AG-AGCAGATC
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGA-A
* *
29690145 G-CATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAA
1 GAAAT-CAATCTTATCTCCCTGAAGTTGCAGTGAAGCAG-CAGAA
* * * * **
29690189 GAAATCAATCCTATCTCCCTAAAGTTGCAGTGGAGC-GGATTA
1 GAAATCAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGAA
** *
29690231 -AAATCAGATCTTATCTCTTTGAAGTTGCA--GAAG-AGCAGATC
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGA-A
* *
29690272 G-CATCCAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAGAA
1 GAAAT-CAATCTTATCTCCCTGAAGTTGCAGTGAAGCAG-CAGAA
* * **
29690316 GAAATCAATCCTATCTCCCTGAAGTTGCAGTGAAGC-GGATTA
1 GAAATCAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGAA
*
29690358 -AAATCAGATCTTATCTCTCTGAAGTTGCAG
1 GAAATCA-ATCTTATCTCCCTGAAGTTGCAG
29690388 AAGAGTAGAT
Statistics
Matches: 286, Mismatches: 49, Indels: 64
0.72 0.12 0.16
Matches are distributed among these distances:
39 1 0.00
40 14 0.05
41 88 0.31
42 93 0.33
43 13 0.05
44 65 0.23
45 12 0.04
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
GAAATCAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGCAGAA
Found at i:29690233 original size:127 final size:127
Alignment explanation
Indices: 29690073--29690433 Score: 616
Period size: 127 Copynumber: 2.8 Consensus size: 127
29690063 CATCCAGTCT
*
29690073 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCA-ATAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGA-AG
*
29690137 AGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
65 AGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
* *
29690200 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTTTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
*
29690265 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAGAAGAAATCAATCC
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
*
29690327 TATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
* * * *
29690392 GTAGATTGCATCCAGTCCTATCTCCCTGAGGTTGCAGTGGAG
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
29690434 TGGATTAAAA
Statistics
Matches: 220, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
127 219 1.00
128 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
Found at i:29691683 original size:3 final size:3
Alignment explanation
Indices: 29691675--29691724 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
29691665 ATTTTTACAC
* *
29691675 TAT TAT TAT CAT CAT TAT TAT TAT TATT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT
29691722 TAT
1 TAT
29691725 ACTTACGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 37 0.84
4 7 0.16
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29691893 original size:27 final size:26
Alignment explanation
Indices: 29691839--29691940 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 26
29691829 TTTTCATAGT
29691839 TTTTATATATATGTATATACATTTATA
1 TTTTATA-ATATGTATATACATTTATA
29691866 TTTTATAATAT-T-TATACATTTTCCATA
1 TTTTATAATATGTATATACA-TTT--ATA
* * * **
29691893 TTATATAATCTATATATATGTTTATACA
1 TTTTATAATATGTATATACATTTAT--A
29691921 TTTTTTATAATATGTATATA
1 --TTTTATAATATGTATATA
29691941 TATATACATA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
24 6 0.10
25 4 0.07
26 6 0.10
27 19 0.32
28 5 0.08
29 4 0.07
30 15 0.25
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTTATAATATGTATATACATTTATA
Found at i:29692023 original size:24 final size:24
Alignment explanation
Indices: 29691992--29692059 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 24
29691982 TTTCATAGTT
29691992 TTTATATATTTAT-ATATGCATATACA
1 TTTATAT-TTTATAATAT-C-TATACA
29692018 TTTATATTTTATAATATCTATACA
1 TTTATATTTTATAATATCTATACA
29692042 TTTTCCATATTTTATAAT
1 -TTT--ATATTTTATAAT
29692060 CTATATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.16
25 9 0.24
26 11 0.29
27 12 0.32
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.54
Consensus pattern (24 bp):
TTTATATTTTATAATATCTATACA
Found at i:29692040 original size:158 final size:153
Alignment explanation
Indices: 29691790--29692103 Score: 479
Period size: 158 Copynumber: 2.0 Consensus size: 153
29691780 TGTTTTTTAA
*
29691790 ATACATATACATATTTATTATTATCATATTATTATTTTATTTTCATAGTTTTTATATATATGTAT
1 ATACATATACATATTTATTATTAT-ATATTATTATTTTATTTTCATAGTTTTTATATATATGCAT
* **
29691855 ATACATTTATATTTTATAATATTTATACATTTTCCATATTATATAATCTATATATATGTTTATAC
65 ATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAAATTTATAC
* *
29691920 ATTTTTTATAATATGTATATATAT
130 ATTCTTTATAATATGCATATATAT
29691944 ATACATATACATATTTTATTATTAT-T-TTATTATTTTATTTTCATAGTTTTTATATATTTATAT
1 ATACATATACATA-TTTATTATTATATATTATTATTTTATTTTCATAG--TTT-T-TA--TATAT
*
29692007 ATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAATCTATATATAAAT
59 ATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAAAT
29692072 TTATACATTCTTTATAATATGCATATATAT
124 TTATACATTCTTTATAATATGCATATATAT
29692102 AT
1 AT
29692104 TCTTACACTA
Statistics
Matches: 146, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
152 20 0.14
153 1 0.01
154 16 0.11
155 12 0.08
156 2 0.01
158 95 0.65
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (153 bp):
ATACATATACATATTTATTATTATATATTATTATTTTATTTTCATAGTTTTTATATATATGCATA
TACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAAATTTATACA
TTCTTTATAATATGCATATATAT
Done.