Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 102 of 120
Found at i:30008548 original size:25 final size:25
Alignment explanation
Indices: 30008520--30008574 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
30008510 AATTAAAAAA
30008520 ATGTAAGTTATGT-AGAT-TGTAAGTT
1 ATGTAAG-T-TGTAAGATATGTAAGTT
*
30008545 ATGTAAGTTGTAAGTTATGTAAGTT
1 ATGTAAGTTGTAAGATATGTAAGTT
30008570 ATGTA
1 ATGTA
30008575 TAATATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 3 0.11
24 4 0.15
25 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (25 bp):
ATGTAAGTTGTAAGATATGTAAGTT
Found at i:30008549 original size:9 final size:9
Alignment explanation
Indices: 30008520--30008659 Score: 80
Period size: 9 Copynumber: 15.6 Consensus size: 9
30008510 AATTAAAAAA
30008520 ATGTAAGTT
1 ATGTAAGTT
*
30008529 ATGT-AGAT
1 ATGTAAGTT
30008537 -TGTAAGTT
1 ATGTAAGTT
30008545 ATGTAAG-T
1 ATGTAAGTT
30008553 -TGTAAGTT
1 ATGTAAGTT
30008561 ATGTAAGTT
1 ATGTAAGTT
*
30008570 ATGTATAATATT
1 ATG--TAA-GTT
30008582 AAT-TAA-TT
1 -ATGTAAGTT
** *
30008590 AACTAACTT
1 ATGTAAGTT
*
30008599 ATGTAATTT
1 ATGTAAGTT
* *
30008608 AAGTATAATATT
1 -A-TGTAA-GTT
30008620 AATGTAAGTT
1 -ATGTAAGTT
30008630 ATGTAAG-T
1 ATGTAAGTT
30008638 -TGTAAGTT
1 ATGTAAGTT
30008646 ATGTAAGTT
1 ATGTAAGTT
30008655 ATGTA
1 ATGTA
30008660 TAATATTAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 30
0.72 0.08 0.21
Matches are distributed among these distances:
7 16 0.15
8 15 0.14
9 49 0.47
10 6 0.06
11 11 0.10
12 6 0.06
13 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.44
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:30008633 original size:31 final size:30
Alignment explanation
Indices: 30008597--30008799 Score: 185
Period size: 31 Copynumber: 6.8 Consensus size: 30
30008587 ATTAACTAAC
30008597 TTATGTAATTTAAGTATAATATTAATGTAAG
1 TTATGTAA-TTAAGTATAATATTAATGTAAG
*
30008628 TTATGTAAGTT--G--TAA-GTT-ATGTAAG
1 TTATGTAA-TTAAGTATAATATTAATGTAAG
* * *
30008653 TTATGT-A-TAA-TATTA-ATTAA-CTAAC
1 TTATGTAATTAAGTATAATATTAATGTAAG
30008678 TTATGTAATTTAAGTATAATATTAATGTAAG
1 TTATGTAA-TTAAGTATAATATTAATGTAAG
*
30008709 TTATGTAATTAATGTATAATATTAATTAATTAAG
1 TTATGTAATTAA-GTATAATATTAA-T--GTAAG
* *
30008743 TCATGTAATTTATGTATAATATTAATGTAAG
1 TTATGTAA-TTAAGTATAATATTAATGTAAG
30008774 TTATGTAATTAATGTATAATATTAAT
1 TTATGTAATTAA-GTATAATATTAAT
30008800 TAATTAANNN
Statistics
Matches: 140, Mismatches: 15, Indels: 34
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.01
24 1 0.01
25 26 0.19
26 4 0.03
27 3 0.02
28 3 0.02
29 5 0.04
30 12 0.09
31 57 0.41
32 1 0.01
33 1 0.01
34 23 0.16
35 3 0.02
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (30 bp):
TTATGTAATTAAGTATAATATTAATGTAAG
Found at i:30008637 original size:85 final size:81
Alignment explanation
Indices: 30008537--30008716 Score: 324
Period size: 81 Copynumber: 2.2 Consensus size: 81
30008527 TTATGTAGAT
30008537 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAACTAACTTATG
1 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTAT-A-A-T-ATTAATTAACTAACTTATG
30008602 TAATTTAAGTATAATATTAA
62 TAATTTAAGTATAATATTAA
30008622 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
1 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
30008687 TTAAGTATAATATTAA
66 TTAAGTATAATATTAA
30008703 TGTAAGTTATGTAA
1 TGTAAGTTATGTAA
30008717 TTAATGTATA
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
81 53 0.56
82 1 0.01
83 1 0.01
84 1 0.01
85 39 0.41
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.44
Consensus pattern (81 bp):
TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
TTAAGTATAATATTAA
Found at i:30008643 original size:16 final size:16
Alignment explanation
Indices: 30008622--30008654 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30008612 ATAATATTAA
30008622 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
30008638 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
30008654 T
1 T
30008655 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:30008682 original size:34 final size:33
Alignment explanation
Indices: 30008639--30008802 Score: 196
Period size: 34 Copynumber: 5.0 Consensus size: 33
30008629 TATGTAAGTT
30008639 GTAAGTTATGTAAGTTATGTATAATATTAATTAA
1 GTAAGTTATGTAA-TTATGTATAATATTAATTAA
* * *
30008673 CTAACTTATGTAATTTAAGTATAATATTAA-T--
1 GTAAGTTATGTAA-TTATGTATAATATTAATTAA
30008704 GTAAGTTATGTAATTAATGTATAATATTAATTAA
1 GTAAGTTATGTAATT-ATGTATAATATTAATTAA
* *
30008738 TTAAGTCATGTAATTTATGTATAATATTAA-T--
1 GTAAGTTATGTAA-TTATGTATAATATTAATTAA
30008769 GTAAGTTATGTAATTAATGTATAATATTAATTAA
1 GTAAGTTATGTAATT-ATGTATAATATTAATTAA
30008803 TTAANNNNNN
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
30 4 0.04
31 49 0.45
32 2 0.02
33 2 0.02
34 51 0.46
35 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (33 bp):
GTAAGTTATGTAATTATGTATAATATTAATTAA
Found at i:30008723 original size:9 final size:9
Alignment explanation
Indices: 30008698--30008789 Score: 51
Period size: 9 Copynumber: 11.0 Consensus size: 9
30008688 TAAGTATAAT
30008698 ATTAATGTA
1 ATTAATGTA
30008707 AGTT-ATGTA
1 A-TTAATGTA
30008716 ATTAATGT-
1 ATTAATGTA
*
30008724 A-TAATATTA
1 ATTAAT-GTA
30008733 ATTAAT-TA
1 ATTAATGTA
* *
30008741 AGTCATGTA
1 ATTAATGTA
*
30008750 ATTTATGT-
1 ATTAATGTA
30008758 A-TAA--T-
1 ATTAATGTA
30008763 ATTAATGTA
1 ATTAATGTA
30008772 AGTT-ATGTA
1 A-TTAATGTA
30008781 ATTAATGTA
1 ATTAATGTA
30008790 TAATATTAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 24
0.68 0.06 0.25
Matches are distributed among these distances:
5 2 0.03
6 3 0.05
7 6 0.09
8 14 0.22
9 32 0.49
10 8 0.12
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (9 bp):
ATTAATGTA
Found at i:30008803 original size:65 final size:65
Alignment explanation
Indices: 30008638--30008806 Score: 286
Period size: 65 Copynumber: 2.6 Consensus size: 65
30008628 TTATGTAAGT
* *
30008638 TGTAAGTTATGTAAGTT-ATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTA
1 TGTAAGTTATGTAA-TTAATGTATAATATTAATTAATTAACTCATGTAATTTAAGTATAATATTA
30008702 A
65 A
* *
30008703 TGTAAGTTATGTAATTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTAATGTATAATATTAATTAATTAACTCATGTAATTTAAGTATAATATTAA
30008768 TGTAAGTTATGTAATTAATGTATAATATTAATTAATTAA
1 TGTAAGTTATGTAATTAATGTATAATATTAATTAATTAA
30008807 NNNNNNNNNN
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
64 2 0.02
65 97 0.98
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (65 bp):
TGTAAGTTATGTAATTAATGTATAATATTAATTAATTAACTCATGTAATTTAAGTATAATATTAA
Found at i:30009082 original size:9 final size:9
Alignment explanation
Indices: 30009068--30009092 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30009058 NNNNNNTAAG
30009068 TTATGTAAT
1 TTATGTAAT
30009077 TTATGTAAT
1 TTATGTAAT
30009086 TTATGTA
1 TTATGTA
30009093 TATATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
TTATGTAAT
Found at i:30011751 original size:20 final size:20
Alignment explanation
Indices: 30011713--30011752 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
30011703 AAATTTTTGT
30011713 TTTTTTATTTCCTTTTTATAA
1 TTTTTTATTT-CTTTTTATAA
30011734 TTTTTTATTT-TTTCTTATA
1 TTTTTTATTTCTTT-TTATA
30011753 CTTTGGTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 5 0.28
21 10 0.56
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTATTTCTTTTTATAA
Found at i:30011791 original size:2 final size:2
Alignment explanation
Indices: 30011784--30011808 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30011774 TAATTAAATC
30011784 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30011809 CATTCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30012145 original size:7 final size:7
Alignment explanation
Indices: 30012103--30012127 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30012093 ATAATTAAGT
30012103 ACCCCAA
1 ACCCCAA
30012110 ACCCCAA
1 ACCCCAA
30012117 ACCCCAA
1 ACCCCAA
30012124 ACCC
1 ACCC
30012128 TACCCCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (7 bp):
ACCCCAA
Found at i:30012293 original size:90 final size:88
Alignment explanation
Indices: 30012129--30012374 Score: 386
Period size: 90 Copynumber: 2.8 Consensus size: 88
30012119 CCCAAACCCT
* * *
30012129 ACCCCTAAACCCTAAACACTATTTAATATATAATTTAAAAAACACTAATTAATCTAAACCCTAAA
1 ACCCCTAACCCCTAAACA-TATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
*
30012194 CCCTCACTCGACCACGAATCACTA
65 CCCTAACTCGACCACGAATCACTA
*
30012218 ACCCCCAACCCCTAAACATAATTTAATATATAAATTAAAAAAACACTAATTAATCTAAATCCTAA
1 ACCCCTAACCCCTAAACAT-ATTTAATATATAAATT-AAAAAACACTAATTAATCTAAATCCTAA
* *
30012283 ACCCTAACTCGACCCCGAATCGCTA
64 ACCCTAACTCGACCACGAATCACTA
30012308 ACCCCTAACCCCTAAACATTATTTAATATATAAA-TAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCTAACCCCTAAACA-TATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
30012372 CCC
65 CCC
30012375 CTAGCTAACC
Statistics
Matches: 146, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
88 33 0.23
89 32 0.22
90 80 0.55
91 1 0.01
ACGTcount: A:0.45, C:0.28, G:0.02, T:0.25
Consensus pattern (88 bp):
ACCCCTAACCCCTAAACATATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAAC
CCTAACTCGACCACGAATCACTA
Found at i:30012397 original size:88 final size:87
Alignment explanation
Indices: 30012116--30012403 Score: 366
Period size: 90 Copynumber: 3.3 Consensus size: 87
30012106 CCAAACCCCA
* * *
30012116 AACCCCAAA-CCCT-ACCCCTAAACCCTAAACACTATTTAATATATAATTTAAAAAACACTAATT
1 AACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAA-ATAAAAAACACTAATT
*
30012179 AATCTAAACCCTAAACCCTCACTC
65 AATCTAAATCCTAAACCCT-ACTC
* * * * * *
30012203 GACCACGAATCACTAACCCCCAACCCCTAAACATAATTTAATATATAAATTAAAAAAACACTAAT
1 AACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAA-T-AAAAAACACTAAT
30012268 TAATCTAAATCCTAAACCCTAACTC
64 TAATCTAAATCCTAAACCCT-ACTC
* * *
30012293 GACCCCGAATCGCTAACCCCTAACCCCTAAACATTATTTAATATATAAATAAAAAACACTAATTA
1 AACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATAAAAAACACTAATTA
30012358 ATCTAAATCCTAAACCCCTAGCT-
66 ATCTAAATCCTAAA-CCCTA-CTC
*
30012381 AACCCTAAATCCCTAACCCCTAA
1 AACCCCAAATCCCTAACCCCTAA
30012404 ACATTATTTA
Statistics
Matches: 176, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
87 6 0.03
88 52 0.30
89 37 0.21
90 81 0.46
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.24
Consensus pattern (87 bp):
AACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATAAAAAACACTAATTA
ATCTAAATCCTAAACCCTACTC
Found at i:30012532 original size:20 final size:20
Alignment explanation
Indices: 30012507--30012550 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
30012497 AATTAACCAA
*
30012507 TAAACCCTATTTCCATAATC
1 TAAACCCTAATTCCATAATC
*
30012527 TAAACCTTAATTCCATAATC
1 TAAACCCTAATTCCATAATC
30012547 TAAA
1 TAAA
30012551 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAACCCTAATTCCATAATC
Found at i:30013158 original size:113 final size:114
Alignment explanation
Indices: 30012959--30013786 Score: 1172
Period size: 114 Copynumber: 7.3 Consensus size: 114
30012949 AGATAAAATG
* * * *
30012959 TTTTTGCGGCGC-TTTACAAAAAACGCCGCTAAAGGCATCAGCATTAGCGGCGCTTATTCA-AAA
1 TTTTTGCGGCGCATTTA-AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TACATAAA
*
30013022 ACGCCGCTAAAGTCCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
64 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
30013073 -TTTTGCGGCACATTTAAAAAAACGCCGCTAACGACCTGAGCATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
*
30013137 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
30013186 -TTTTGCGGCGCATTTAAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAA
1 TTTTTGCGGCGCATTT-AAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAA
* * * *
30013250 CGTCACTAAAGACCCCAAAAACTCATAAAACGGTGCCGTTGGGTTTAGGC
65 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * * *
30013300 TTTTTGCGGCGCTTTTGAGAAAACGCCGCTAAAGACCTCAGCATTAGCGGCGCTTT--ATAAATG
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAA-A
30013363 CGCCGCTAAAGACCCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
65 CGCCGCTAAAGA-CCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
30013414 TTTTTGCGGCGCATTTAAAAAAACGCCACTAAAGACCTGAACATTAGCGGCGCTTTACAT-AAAC
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
* *
30013478 GCCGCGAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGAGCTTAGGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTA-GGC
* * *
30013528 TTTTTGCGGCGC-TTTAAAAAAAACACCGCTAAAGACATGAGCATTAGCGGCACTTTACAT-AAA
1 TTTTTGCGGCGCATTT-AAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAA
* * * *
30013591 CGCCACTAAACACCCC-AAAACTCAGAAAACGGTGCCGTTGGGTTTAGAC
65 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
30013640 TTTTTGCGGCGCTTTTAAAACAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTACAGAAAA
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGC-TTTACATAAAA
* * * * *
30013705 CGCCGCTAAAGACCCCAAAAAATCAGAAAACGGTGTCGTTTGTCTTTGGC
65 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
30013755 TTTTTGCGGCGCTTTTATAAAAACGCCGCTAA
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAA
30013787 TGCTTATTTT
Statistics
Matches: 642, Mismatches: 58, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
112 55 0.09
113 194 0.30
114 319 0.50
115 72 0.11
116 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (114 bp):
TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:30015864 original size:45 final size:43
Alignment explanation
Indices: 30015809--30016742 Score: 466
Period size: 44 Copynumber: 21.0 Consensus size: 43
30015799 AAGACTTGTA
30015809 TCTTCGATCTACTTCGCCACCGATATGGGAAGACAAGATCTG-TT
1 TCTTCGATCTACTTC-CCACC-ATATGGGAAGACAAGATCTGCTT
* * * ***
30015853 GTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 -TCTTCGATCTACTTCCCACC-ATATGGGAAGACAAGATCTGCTT
*
30015898 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGACCTGCTT
1 TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCTGCTT
* * *** *
30015943 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCCCACC-ATATGGGAAGACAAGATCTGCTT
* * * * *
30015987 TCTTCGATCTA-TTCCACTGCCGACCA-GGG-AGA-TAGAAT-TACTG
1 TCTTCGATCTACTTCC-C-ACC-A-TATGGGAAGACAAG-ATCTGCTT
* * * * **
30016030 GCTTCAATGTAC-TCCACTGTAACC-TCA-GGGAGGTA-AA-ATCTGCCA
1 TCTTCGATCTACTTCC-C----ACCAT-ATGGGAAG-ACAAGATCTGCTT
* * *
30016075 TCTTCGATCTGCTTCGCCATCAGTATGGGAAGACAAGATCTGCTG
1 TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCTGCTT
* * * *** *
30016120 TCTTTGATCTACTTCACGCCAATACATGAAGACAATATCTGCTT
1 TCTTCGATCTACTTCCCACC-ATATGGGAAGACAAGATCTGCTT
*
30016164 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG-TA
1 TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCT-GCTT
* * * ***
30016209 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG-TT
1 TCTTCGATCTACTTCCCACC-ATATGGGAAGACAAGATCTGCTT
* * * *
30016252 CTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGACCTG-TT
1 -TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCTGCTT
* * * ***
30016297 ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 -TCTTCGATCTACTTCCCACCA-TATGGGAAGACAAGATCTGCTT
** * *
30016342 TCTTCGATCTGTTTTGCCACTAGTATGGGAAGACAAGATCTG-TT
1 TCTTCGATCT-ACTTCCCACCA-TATGGGAAGACAAGATCTGCTT
* * * * * ***
30016386 ACCTTTGATCTATTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 -TCTTCGATCTACTTCCCACCA-TATGGGAAGACAAGATCTGCTT
**
30016431 TCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTG-TT
1 TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCTGCTT
* * * *** *
30016475 ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTT
1 -TCTTCGATCTACTTCCCACCA-TATGGGAAGACAAGATCTGCTT
* **
30016520 TTTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTG-TT
1 TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCTGCTT
* * *** *
30016564 ATCTTTGATCTACTT-CAAGCCAGTACATGAAGACAAGGTCTGCTT
1 -TCTTCGATCTACTTCCCA-CCA-TATGGGAAGACAAGATCTGCTT
* *
30016609 TCTTCGATCTATTTCGCCACCAGTATGGGAAGACAAGATTTG-TT
1 TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCTGCTT
* * * ***
30016653 ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 -TCTTCGATCTACTTCCCACCA-TATGGGAAGACAAGATCTGCTT
**
30016698 TCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTC-CCACCA-TATGGGAAGACAAGATCTGCTT
30016743 CTTTTTTTAA
Statistics
Matches: 672, Mismatches: 170, Indels: 94
0.72 0.18 0.10
Matches are distributed among these distances:
42 2 0.00
43 27 0.04
44 318 0.47
45 313 0.47
46 11 0.02
47 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (43 bp):
TCTTCGATCTACTTCCCACCATATGGGAAGACAAGATCTGCTT
Found at i:30015960 original size:89 final size:89
Alignment explanation
Indices: 30015809--30016739 Score: 1157
Period size: 89 Copynumber: 10.5 Consensus size: 89
30015799 AAGACTTGTA
*
30015809 TCTTCGATCTACTTCGCCACC-GATATGGGAAGACAAGATCTGTTGTCTTTGATCTACTTCACGC
1 TCTTCGATCTACTTCGCCACCAG-TATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGC
30015873 CAATACATGAAGACAAGATCTGCTT
65 CAATACATGAAGACAAGATCTGCTT
* * *
30015898 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGACCTGCTT-TCTTCGATCTACTTCACGC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TTATCTTTGATCTACTTCACGC
*
30015962 CAATACATGAAGACAAGATCTGCTA
65 CAATACATGAAGACAAGATCTGCTT
* ** * ** ** ** * *
30015987 TCTTCGATCTA-TTC-CACTGCCGACCA-GGG-AGA-TAGAAT-TACTGGCTTCAATGTACTCCA
1 TCTTCGATCTACTTCGC-C-ACC-AGTATGGGAAGACAAG-ATCTGTTATCTTTGATCTACTTCA
* * * ** * **
30016046 CTG-TAACCT-CAGGGAGGTAAAATCTGCCA
62 C-GCCAA--TACATGAAGACAAGATCTGCTT
* * * *
30016075 TCTTCGATCTGCTTCGCCATCAGTATGGGAAGACAAGATCTGCTGTCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
*
30016140 AATACATGAAGACAATATCTGCTT
66 AATACATGAAGACAAGATCTGCTT
30016164 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG-TATCTTTGATCTACTTCACGC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-GTTATCTTTGATCTACTTCACGC
30016228 CAATACATGAAGACAAGATCTG-TT
65 CAATACATGAAGACAAGATCTGCTT
* * * * *
30016252 CTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGACCTGTTATCTTTGATCTACTTCACGC
1 -TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGC
*
30016317 CAGTACATGAAGACAAGATCTGCTT
65 CAATACATGAAGACAAGATCTGCTT
** * * * *
30016342 TCTTCGATCTGTTTTGCCACTAGTATGGGAAGACAAGATCTGTTACCTTTGATCTATTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
*
30016407 AGTACATGAAGACAAGATCTGCTT
66 AATACATGAAGACAAGATCTGCTT
**
30016431 TCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
* *
30016496 AGTACATGAAGACAAGATCCGCTT
66 AATACATGAAGACAAGATCTGCTT
* ** *
30016520 TTTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCAAGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
* *
30016585 AGTACATGAAGACAAGGTCTGCTT
66 AATACATGAAGACAAGATCTGCTT
* *
30016609 TCTTCGATCTATTTCGCCACCAGTATGGGAAGACAAGATTTGTTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
*
30016674 AGTACATGAAGACAAGATCTGCTT
66 AATACATGAAGACAAGATCTGCTT
**
30016698 TCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTG
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG
30016740 CTTCTTTTTT
Statistics
Matches: 741, Mismatches: 79, Indels: 44
0.86 0.09 0.05
Matches are distributed among these distances:
86 1 0.00
87 21 0.03
88 41 0.06
89 649 0.88
90 29 0.04
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
AATACATGAAGACAAGATCTGCTT
Found at i:30017856 original size:17 final size:17
Alignment explanation
Indices: 30017834--30017869 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
30017824 TTCGTCGATG
*
30017834 CCCCAAAATGTCGCCTA
1 CCCCAAAATGCCGCCTA
30017851 CCCCAAAATGCCGCCTA
1 CCCCAAAATGCCGCCTA
30017868 CC
1 CC
30017870 TTTTCCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.47, G:0.11, T:0.14
Consensus pattern (17 bp):
CCCCAAAATGCCGCCTA
Found at i:30018063 original size:13 final size:14
Alignment explanation
Indices: 30018045--30018093 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
30018035 CCTTAGCCTC
30018045 TCCATTTT-ACTTT
1 TCCATTTTCACTTT
*
30018058 TCCATTTTTCAGTTT
1 TCCA-TTTTCACTTT
30018073 T-CATTTTCACTTT
1 TCCATTTTCACTTT
*
30018086 TTCATTTT
1 TCCATTTT
30018094 TCATCTCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 14 0.45
14 12 0.39
15 5 0.16
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.63
Consensus pattern (14 bp):
TCCATTTTCACTTT
Found at i:30018073 original size:7 final size:7
Alignment explanation
Indices: 30018055--30018097 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
30018045 TCCATTTTAC
*
30018055 TTTTCCA
1 TTTTTCA
30018062 TTTTTCA
1 TTTTTCA
*
30018069 GTTTTCA
1 TTTTTCA
30018076 -TTTTCA
1 TTTTTCA
30018082 CTTTTTCA
1 -TTTTTCA
30018090 TTTTTCA
1 TTTTTCA
30018097 T
1 T
30018098 CTCATCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 20 0.62
8 6 0.19
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTTCA
Found at i:30018077 original size:14 final size:15
Alignment explanation
Indices: 30018055--30018096 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30018045 TCCATTTTAC
30018055 TTTTCCATTTTTCA-G
1 TTTT-CATTTTTCACG
*
30018070 TTTTCA-TTTTCACT
1 TTTTCATTTTTCACG
30018084 TTTTCATTTTTCA
1 TTTTCATTTTTCA
30018097 TCTCATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 8 0.33
15 10 0.42
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTCATTTTTCACG
Found at i:30020809 original size:4 final size:4
Alignment explanation
Indices: 30020800--30020825 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30020790 GTAACGGTGT
30020800 TTGG TTGG TTGG TTGG TTGG TTGG TT
1 TTGG TTGG TTGG TTGG TTGG TTGG TT
30020826 TCCAGGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (4 bp):
TTGG
Found at i:30020970 original size:13 final size:13
Alignment explanation
Indices: 30020952--30020977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30020942 GTTCAATTTT
30020952 TTTACTAGAAAAC
1 TTTACTAGAAAAC
30020965 TTTACTAGAAAAC
1 TTTACTAGAAAAC
30020978 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:30023187 original size:25 final size:25
Alignment explanation
Indices: 30023132--30023187 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
30023122 ATAAAAGTGT
* * *
30023132 TATATATATTATATAAAGAAATATG
1 TATATATACTATATAAAAAAATACG
30023157 TATATATACTATATAAAAAAATACG
1 TATATATACTATATAAAAAAATACG
*
30023182 TGTATA
1 TATATA
30023188 AATATAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (25 bp):
TATATATACTATATAAAAAAATACG
Found at i:30023187 original size:27 final size:25
Alignment explanation
Indices: 30023132--30023179 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
30023122 ATAAAAGTGT
* *
30023132 TATATATATTATATAAAGAAATATG
1 TATATATACTATATAAAAAAATATG
30023157 TATATATACTATATAAAAAAATA
1 TATATATACTATATAAAAAAATA
30023180 CGTGTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
TATATATACTATATAAAAAAATATG
Found at i:30027797 original size:42 final size:42
Alignment explanation
Indices: 30027697--30027853 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 42
30027687 TGTGATCTCG
*
30027697 TGTAAGACCAC-GTTTGGGACATTGGCATCG-ATTTGAGATTTACA
1 TGTAAGACC-CTGTCTGGGACATTGGCATCGTATTT--GATTT-CA
* * * *
30027741 TGTAAGACCATGTCTAGGACATTGGCATCGTATATGATTTCG
1 TGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTTCA
* *
30027783 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCCTGTCTGGGACATTGGCATCG-TATTTGATTTCA
* * **
30027826 TGTAAGATCATGTCTGGGATGTTGGCAT
1 TGTAAGACCCTGTCTGGGACATTGGCAT
30027854 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 28 0.30
43 37 0.39
44 26 0.28
45 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (42 bp):
TGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTTCA
Found at i:30028360 original size:2 final size:2
Alignment explanation
Indices: 30028347--30028386 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
30028337 GGATTTCATG
*
30028347 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30028387 GGTGTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30033810 original size:10 final size:10
Alignment explanation
Indices: 30033795--30033951 Score: 50
Period size: 10 Copynumber: 16.4 Consensus size: 10
30033785 ACATGTGACA
30033795 AAAAAATTAT
1 AAAAAATTAT
30033805 -AAAAA--AT
1 AAAAAATTAT
*
30033812 -AAAAATCA-
1 AAAAAATTAT
30033820 ATAAAAATTAT
1 A-AAAAATTAT
30033831 --AAAATTAT
1 AAAAAATTAT
* **
30033839 TAAACTTTAAT
1 AAAAAATT-AT
30033850 AAAAAA-TATT
1 AAAAAATTA-T
* *
30033860 TAAAATTTACT
1 AAAAAATTA-T
*
30033871 A-AAAATTAG
1 AAAAAATTAT
**
30033880 AAAAAAAAAT
1 AAAAAATTAT
**
30033890 ATAAAAATCGT
1 A-AAAAATTAT
30033901 AAAAAA-TAT
1 AAAAAATTAT
*
30033910 -AAAAATTGT
1 AAAAAATTAT
**
30033919 AAAATTTTAT
1 AAAAAATTAT
*
30033929 -AAAAATCAT
1 AAAAAATTAT
30033938 AAAAAATTAT
1 AAAAAATTAT
30033948 AAAA
1 AAAA
30033952 TCTATCAAAA
Statistics
Matches: 104, Mismatches: 28, Indels: 30
0.64 0.17 0.19
Matches are distributed among these distances:
7 7 0.07
8 13 0.12
9 17 0.16
10 52 0.50
11 15 0.14
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:30033832 original size:9 final size:9
Alignment explanation
Indices: 30033796--30033951 Score: 75
Period size: 9 Copynumber: 16.4 Consensus size: 9
30033786 CATGTGACAA
30033796 AAAAATTAT
1 AAAAATTAT
30033805 AAAAA--AT
1 AAAAATTAT
*
30033812 AAAAATCAAT
1 AAAAAT-TAT
30033822 AAAAATTAT
1 AAAAATTAT
30033831 -AAAATTATT
1 AAAAATTA-T
**
30033840 AAACTTTAAT
1 AAAAATT-AT
*
30033850 AAAAAATATTT
1 -AAAAAT-TAT
*
30033861 AAAATTTACT
1 AAAAATTA-T
*
30033871 AAAAATTAGAAA
1 AAAAATT---AT
*
30033883 AAAAAATAT
1 AAAAATTAT
**
30033892 AAAAATCGT
1 AAAAATTAT
*
30033901 AAAAAATAT
1 AAAAATTAT
*
30033910 AAAAATTGT
1 AAAAATTAT
*
30033919 AAAATTTTAT
1 AAAA-ATTAT
*
30033929 AAAAATCAT
1 AAAAATTAT
30033938 AAAAAATTAT
1 -AAAAATTAT
30033948 AAAA
1 AAAA
30033952 TCTATCAAAA
Statistics
Matches: 108, Mismatches: 25, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
7 7 0.06
8 7 0.06
9 40 0.37
10 40 0.37
11 6 0.06
12 7 0.06
13 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:30033906 original size:18 final size:18
Alignment explanation
Indices: 30033883--30033951 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
30033873 AAATTAGAAA
30033883 AAAAAATATAAAAATCGT
1 AAAAAATATAAAAATCGT
*
30033901 AAAAAATATAAAAATTGT
1 AAAAAATATAAAAATCGT
** *
30033919 AAAATTTTATAAAAATCAT
1 AAAA-AATATAAAAATCGT
30033938 AAAAAATTATAAAA
1 AAAAAA-TATAAAA
30033952 TCTATCAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 21 0.50
19 21 0.50
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAAATATAAAAATCGT
Found at i:30033961 original size:29 final size:27
Alignment explanation
Indices: 30033883--30033963 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 27
30033873 AAATTAGAAA
* *
30033883 AAAAAATATAAAAATCGTA-AAAAATAT
1 AAAAATTATAAAATTC-TATAAAAATAT
* *
30033910 AAAAATTGTAAAATTTTATAAAAATCAT
1 AAAAATTATAAAATTCTATAAAAAT-AT
30033938 AAAAAATTATAAAA-TCTATCAAAAAT
1 -AAAAATTATAAAATTCTAT-AAAAAT
30033964 GCCCTTTAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.05
27 18 0.41
28 6 0.14
29 18 0.41
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAATTATAAAATTCTATAAAAATAT
Found at i:30033963 original size:19 final size:19
Alignment explanation
Indices: 30033882--30033951 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
30033872 AAAATTAGAA
* *
30033882 AAAAAAATATAAAAATCGT
1 AAAAAATTATAAAAATCAT
**
30033901 AAAAAA-TATAAAAATTGT
1 AAAAAATTATAAAAATCAT
**
30033919 AAAATTTTATAAAAATCAT
1 AAAAAATTATAAAAATCAT
30033938 AAAAAATTATAAAA
1 AAAAAATTATAAAA
30033952 TCTATCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAAATTATAAAAATCAT
Found at i:30034089 original size:18 final size:18
Alignment explanation
Indices: 30034066--30034108 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
30034056 ATATGTGGCA
30034066 AAAAATAATA-AAAACAAT
1 AAAAATAATAGAAAA-AAT
*
30034084 AAAAATTATAGAAAAAAT
1 AAAAATAATAGAAAAAAT
30034102 ACAAAAT
1 A-AAAAT
30034109 GTTTCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAATAATAGAAAAAAT
Found at i:30034231 original size:9 final size:9
Alignment explanation
Indices: 30034219--30034291 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
30034209 TTTTCTATTT
*
30034219 TTTTATATA
1 TTTTATAAA
30034228 TTTTATAAA
1 TTTTATAAA
*
30034237 TTTT-TACCAT
1 TTTTATA--AA
30034247 TTTTATAAA
1 TTTTATAAA
*
30034256 ATTTA-AAA
1 TTTTATAAA
*
30034264 TTTTTATAATT
1 -TTTTATAA-A
*
30034275 TTTTATGAA
1 TTTTATAAA
30034284 TTTTATAA
1 TTTTATAA
30034292 TCTTTTTCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
8 5 0.10
9 28 0.57
10 14 0.29
11 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTATAAA
Found at i:30034240 original size:19 final size:18
Alignment explanation
Indices: 30034204--30034291 Score: 68
Period size: 19 Copynumber: 4.7 Consensus size: 18
30034194 AAATTGTATA
* **
30034204 TATATTTTTCTATTTTTT
1 TATATTTTTATAAATTTT
30034222 TATATATTTTATAAATTTT
1 TATAT-TTTTATAAATTTT
* *
30034241 TACCATTTTTATAAAATTT
1 TA-TATTTTTATAAATTTT
* * *
30034260 AAAATTTTTATAATTTTT
1 TATATTTTTATAAATTTT
*
30034278 TATGAATTTTATAA
1 TAT-ATTTTTATAA
30034292 TCTTTTTCTA
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
18 19 0.35
19 34 0.62
20 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (18 bp):
TATATTTTTATAAATTTT
Found at i:30034250 original size:28 final size:28
Alignment explanation
Indices: 30034218--30034291 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
30034208 TTTTTCTATT
*
30034218 TTTTTATATATTTTATAAATTTTTACCA
1 TTTTTATATATTTTATAAATTTTTACAA
* * *
30034246 TTTTTATAAAATTTA-AAATTTTTATAA
1 TTTTTATATATTTTATAAATTTTTACAA
30034273 TTTTT-TATGAATTTTATAA
1 TTTTTATAT--ATTTTATAA
30034292 TCTTTTTCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
26 2 0.05
27 15 0.41
28 18 0.49
29 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTTTATATATTTTATAAATTTTTACAA
Found at i:30034287 original size:56 final size:58
Alignment explanation
Indices: 30034149--30034339 Score: 162
Period size: 60 Copynumber: 3.3 Consensus size: 58
30034139 CTTTTACGAA
* * * * * *
30034149 TTTTATATTTCTTTACATTTTTTATCATTTTCTTAC-AA-CTTTATAAAATTGTATATATAT
1 TTTTATATTTTTTTATATATTTTATAATCTT-TTACTAATTTTTATAAAATT-TA-A-ATAT
* *
30034209 TTTTCTATTTTTTTATATATTTTATAAAT-TTTTAC-CATTTTTATAAAATTTAAA-AT
1 TTTTATATTTTTTTATATATTTTAT-AATCTTTTACTAATTTTTATAAAATTTAAATAT
* * *
30034265 TTTTATAATTTTTTATGA-ATTTTATAATCTTTTTCTAATTTTAATAAAA-TTAAATAT
1 TTTTATATTTTTTTAT-ATATTTTATAATCTTTTACTAATTTTTATAAAATTTAAATAT
30034322 TTCTTATATTTTATTTAT
1 TT-TTATATTTT-TTTAT
30034340 TAAAATTTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
55 3 0.03
56 33 0.30
57 17 0.15
58 9 0.08
59 12 0.11
60 34 0.31
61 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (58 bp):
TTTTATATTTTTTTATATATTTTATAATCTTTTACTAATTTTTATAAAATTTAAATAT
Found at i:30034292 original size:19 final size:19
Alignment explanation
Indices: 30034265--30034307 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
30034255 AATTTAAAAT
30034265 TTTTATAAT-TTTTTATGAA
1 TTTTATAATCTTTTTAT-AA
*
30034284 TTTTATAATCTTTTTCTAA
1 TTTTATAATCTTTTTATAA
30034303 TTTTA
1 TTTTA
30034308 ATAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATAATCTTTTTATAA
Found at i:30034298 original size:11 final size:10
Alignment explanation
Indices: 30034124--30034306 Score: 50
Period size: 9 Copynumber: 18.8 Consensus size: 10
30034114 TTTTGGTATG
30034124 ATAA-TTTTT
1 ATAATTTTTT
30034133 ATAATTCTTTT
1 ATAATT-TTTT
*
30034144 ACGAA--TTTT
1 A-TAATTTTTT
30034153 AT-ATTTCTTT
1 ATAATTT-TTT
*
30034163 A-CATTTTTT
1 ATAATTTTTT
*
30034172 ATCATTTTCTT
1 ATAATTTT-TT
* * *
30034183 ACAACTTTAT
1 ATAATTTTTT
* * *
30034193 AAAATTGTAT
1 ATAATTTTTT
30034203 ATATATTTTTCT
1 ATA-ATTTTT-T
30034215 AT--TTTTTT
1 ATAATTTTTT
*
30034223 AT-ATATTTT
1 ATAATTTTTT
*
30034232 ATAAATTTTT
1 ATAATTTTTT
**
30034242 ACCA-TTTTT
1 ATAATTTTTT
**
30034251 ATAA-AATTT
1 ATAATTTTTT
*
30034260 A-AAATTTTT
1 ATAATTTTTT
30034269 ATAATTTTTT
1 ATAATTTTTT
30034279 ATGAA--TTTT
1 AT-AATTTTTT
30034288 ATAATCTTTTT
1 ATAAT-TTTTT
*
30034299 CTAATTTT
1 ATAATTTT
30034307 AATAAAATTA
Statistics
Matches: 130, Mismatches: 25, Indels: 37
0.68 0.13 0.19
Matches are distributed among these distances:
7 1 0.01
8 7 0.05
9 47 0.36
10 44 0.34
11 26 0.20
12 5 0.04
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:30038022 original size:35 final size:35
Alignment explanation
Indices: 30037976--30038047 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
30037966 TTTTAGATTT
* *
30037976 TTCCGAATCAAACTAAAAGTTTCGAGAATAATTCC
1 TTCCGAATCAAACTAAAAGATTCAAGAATAATTCC
30038011 TTCCGAATCAAACTAAAAGATTCAAGAATAATTCC
1 TTCCGAATCAAACTAAAAGATTCAAGAATAATTCC
30038046 TT
1 TT
30038048 TTGAGTGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (35 bp):
TTCCGAATCAAACTAAAAGATTCAAGAATAATTCC
Found at i:30038888 original size:31 final size:31
Alignment explanation
Indices: 30038853--30038923 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
30038843 TATTTAAATG
*
30038853 TATACAATTGAATCCA-GATTAAAATTTTATA
1 TATACAATTGAA-CCACAATTAAAATTTTATA
* *
30038884 TATACATTTGAACCACAATTAAAATTTTATT
1 TATACAATTGAACCACAATTAAAATTTTATA
*
30038915 TATATAATT
1 TATACAATT
30038924 ATACAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (31 bp):
TATACAATTGAACCACAATTAAAATTTTATA
Found at i:30039060 original size:2 final size:2
Alignment explanation
Indices: 30039053--30039080 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30039043 ATTTACATAC
30039053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30039081 TAAAAAGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30041325 original size:10 final size:10
Alignment explanation
Indices: 30041312--30041345 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
30041302 TTTTTAAATT
30041312 AAAAATTTAA
1 AAAAATTTAA
*
30041322 AAAATTTTAA
1 AAAAATTTAA
30041332 AAAAATATTAA
1 AAAAAT-TTAA
30041343 AAA
1 AAA
30041346 TATAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:30041346 original size:20 final size:21
Alignment explanation
Indices: 30041312--30041359 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
30041302 TTTTTAAATT
*
30041312 AAAAAT-TTAAAAAATTTTAA-
1 AAAAATATTAAAAAA-TATAAG
30041332 AAAAATATT-AAAAATATAAG
1 AAAAATATTAAAAAATATAAG
30041352 AAAAATAT
1 AAAAATAT
30041360 CTTTTAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 4 0.16
20 19 0.76
21 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATATTAAAAAATATAAG
Found at i:30041930 original size:11 final size:11
Alignment explanation
Indices: 30041912--30041945 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
30041902 GCACACAAAC
30041912 AATAATAAAAT
1 AATAATAAAAT
*
30041923 ATTAAT-AAAT
1 AATAATAAAAT
30041933 AATAATAAAAT
1 AATAATAAAAT
30041944 AA
1 AA
30041946 GCAAATCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:30045568 original size:21 final size:20
Alignment explanation
Indices: 30045543--30045583 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
30045533 TGTCCCAACA
*
30045543 AAACAGTTAGAACTATAAATC
1 AAACAATTAGAA-TATAAATC
*
30045564 AAACAATTAGTATATAAATC
1 AAACAATTAGAATATAAATC
30045584 TCTGAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (20 bp):
AAACAATTAGAATATAAATC
Found at i:30049576 original size:20 final size:20
Alignment explanation
Indices: 30049547--30049586 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30049537 ATTAAACAAG
30049547 AAGAAAATAG-TAAGAAAATA
1 AAGAAAATAGATAA-AAAATA
*
30049567 AAGAAGATAGATAAAAAATA
1 AAGAAAATAGATAAAAAATA
30049587 TATATGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
AAGAAAATAGATAAAAAATA
Found at i:30049883 original size:18 final size:19
Alignment explanation
Indices: 30049860--30049897 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30049850 AACAAAAATG
30049860 AATGAAT-TG-ATTCTATAT
1 AATGAATATGCATT-TATAT
30049878 AATGAATATGCATTTATAT
1 AATGAATATGCATTTATAT
30049897 A
1 A
30049898 GGCAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
AATGAATATGCATTTATAT
Found at i:30051336 original size:20 final size:20
Alignment explanation
Indices: 30051293--30051336 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
30051283 ATAAATAAAT
*
30051293 TAAATTTTATAAAAATATTC
1 TAAATTTTATAAAAATATCC
*
30051313 TAAATTTTTTAAAAA-ATCC
1 TAAATTTTATAAAAATATCC
30051332 ATAAA
1 -TAAA
30051337 CAGCTCAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATTTTATAAAAATATCC
Found at i:30057743 original size:9 final size:9
Alignment explanation
Indices: 30057729--30057756 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
30057719 TTTTGTTACA
30057729 ACAATTAAT
1 ACAATTAAT
30057738 ACAATTAAT
1 ACAATTAAT
30057747 ACAATTAAT
1 ACAATTAAT
30057756 A
1 A
30057757 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:30057772 original size:68 final size:66
Alignment explanation
Indices: 30057699--30057840 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
30057689 TCAAGTTTGT
*
30057699 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
30057764 AAA
64 AAA
30057767 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
30057832 T
66 A
30057833 TTTACTAA
1 TTTACTAA
30057841 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:30057850 original size:16 final size:16
Alignment explanation
Indices: 30057829--30057870 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
30057819 AATAATTTGA
* *
30057829 TAATTTTACTAACAAT
1 TAATTTTAATAAAAAT
30057845 TAATTTTAATAAAAAT
1 TAATTTTAATAAAAAT
*
30057861 TAGTTTTAAT
1 TAATTTTAAT
30057871 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAAAAAT
Found at i:30057862 original size:59 final size:67
Alignment explanation
Indices: 30057699--30057862 Score: 218
Period size: 68 Copynumber: 2.5 Consensus size: 67
30057689 TCAAGTTTGT
**
30057699 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTAATACAACAATTAATACAATTAATACAATTAATAATTTGAT
30057764 AAA
65 AAA
*
30057767 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTAATACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
30057830 AAT
65 AAA
30057833 TTTACTAA-C-AA-TTA-ATTTTAATA-AA-AATTA
1 TTTACTAATCAAAGTTAGATTTTAATACAACAATTA
30057863 GTTTTAATTT
Statistics
Matches: 93, Mismatches: 3, Indels: 9
0.89 0.03 0.09
Matches are distributed among these distances:
59 5 0.05
60 2 0.02
61 8 0.09
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 44 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (67 bp):
TTTACTAATCAAAGTTAGATTTTAATACAACAATTAATACAATTAATACAATTAATAATTTGATA
AA
Found at i:30057890 original size:23 final size:22
Alignment explanation
Indices: 30057844--30057899 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
30057834 TTACTAACAA
* *
30057844 TTAATTTTAATAAAAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
30057866 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTA-ATAAAAAATAATT
30057889 TTAATTTTAAT
1 TTAATTTTAAT
30057900 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:30059311 original size:23 final size:25
Alignment explanation
Indices: 30059279--30059324 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
30059269 GTGGAAATTG
30059279 AATTAGAAGCTGAAT-AATATATGA
1 AATTAGAAGCTGAATGAATATATGA
30059303 AATTA-AAGCTGAATGAATATAT
1 AATTAGAAGCTGAATGAATATAT
30059325 TTTAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.30
Consensus pattern (25 bp):
AATTAGAAGCTGAATGAATATATGA
Found at i:30064498 original size:32 final size:32
Alignment explanation
Indices: 30064453--30064529 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
30064443 TTGCCTCCTA
*
30064453 AACTTGTC-CAAAAGTATCTAGTTGATACCGG
1 AACTTGTCAAAAAAGTATCTAGTTGATACCGG
* * * **
30064484 AACTTGTCAAAAAAGTATGTAGTTGGTTCTTG
1 AACTTGTCAAAAAAGTATCTAGTTGATACCGG
30064516 AACTTGTCAAAAAA
1 AACTTGTCAAAAAA
30064530 ATATTATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 8 0.21
32 31 0.79
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (32 bp):
AACTTGTCAAAAAAGTATCTAGTTGATACCGG
Found at i:30065744 original size:77 final size:77
Alignment explanation
Indices: 30065658--30065812 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
30065648 AAAGAATAAT
30065658 TTATTTTTGGGTATTTTACTAAAAAAGGCCCATTTCCAACATTATTTTCAAAAATGAGTCATTTA
1 TTATTTTTGGGTATTTTACTAAAAAAGGCCCATTTCCAACATTATTTTCAAAAATGAGTCATTTA
30065723 AAAGATTATTTC
66 AAAGATTATTTC
30065735 TTATTTTTGGGTATTTTACTAAAAAAGGCCCATTTCCAACATTATTTTCAAAAATGAGTCATTTA
1 TTATTTTTGGGTATTTTACTAAAAAAGGCCCATTTCCAACATTATTTTCAAAAATGAGTCATTTA
30065800 AAAGATTATTTC
66 AAAGATTATTTC
30065812 T
1 T
30065813 CAGAATGGGC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (77 bp):
TTATTTTTGGGTATTTTACTAAAAAAGGCCCATTTCCAACATTATTTTCAAAAATGAGTCATTTA
AAAGATTATTTC
Found at i:30066073 original size:28 final size:29
Alignment explanation
Indices: 30066027--30066093 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
30066017 GAGTTTAGGG
*
30066027 TTAAGGTTTTTAAAAAAATAAATTAAGGT
1 TTAAGGTTTTTAAAAAAATAAAGTAAGGT
* * * *
30066056 TTAGGGTTTTT-AATAAATATAGTAGGGT
1 TTAAGGTTTTTAAAAAAATAAAGTAAGGT
30066084 TTAAGGTTTT
1 TTAAGGTTTT
30066094 AAGATTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.43
Consensus pattern (29 bp):
TTAAGGTTTTTAAAAAAATAAAGTAAGGT
Found at i:30066412 original size:156 final size:157
Alignment explanation
Indices: 30066249--30066556 Score: 469
Period size: 156 Copynumber: 2.0 Consensus size: 157
30066239 GCTTCTAGCA
* *
30066249 GGACGCTTTTTTTGTGCAATTGATTCTGAAAAAATAATTT-TAAGAAGATGGTTCTGAAAAAATA
1 GGACGCTTTTTTTGTACAATTGATTCTGAAAAAATAATTTCGAA-AAGATGGTTCTGAAAAAATA
* *
30066313 TCTCGGAATTCACGGGAAATCTTATAGTTAGGGATGAAAAACGCTTCAAG-CAGGATACACTGTC
65 TCTCGGAATTCACGGGAAATCTGATAGTTAGGGATGAAAAACACTTCAAGTC-GGATACACTGTC
30066377 AGCAAAAGTACTG-AAAAAGCTCCCAGTT
129 AGCAAAAGTACTGAAAAAAGCTCCCAGTT
* *
30066405 GGACGCTTTTTTTGTACAGTTGATTCTGAAAAAATAATTTCGAAAAGATGGTTTTGAAAAAATAT
1 GGACGCTTTTTTTGTACAATTGATTCTGAAAAAATAATTTCGAAAAGATGGTTCTGAAAAAATAT
* * * * *
30066470 CTCGGGATTCATGGGAAATCTGATAGTTGGGGTTGAAAAACACTTCAAGTCGGATGCACTGTCAG
66 CTCGGAATTCACGGGAAATCTGATAGTTAGGGATGAAAAACACTTCAAGTCGGATACACTGTCAG
*
30066535 CAAATGTACTGAAAAAAGCTCC
131 CAAAAGTACTGAAAAAAGCTCC
30066557 TAATTGGATG
Statistics
Matches: 137, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
156 124 0.91
157 13 0.09
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (157 bp):
GGACGCTTTTTTTGTACAATTGATTCTGAAAAAATAATTTCGAAAAGATGGTTCTGAAAAAATAT
CTCGGAATTCACGGGAAATCTGATAGTTAGGGATGAAAAACACTTCAAGTCGGATACACTGTCAG
CAAAAGTACTGAAAAAAGCTCCCAGTT
Found at i:30070575 original size:30 final size:29
Alignment explanation
Indices: 30070513--30070575 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
30070503 ACTATTCCAG
** * *
30070513 TAAATAATATTTTAAGTGGCCCATTTTCA
1 TAAATAATATTAGAAATGGCCCATTTTAA
*
30070542 TAAATAATATTAGAAATGGGCCCTTTTTAA
1 TAAATAATATTAGAAAT-GGCCCATTTTAA
30070572 TAAA
1 TAAA
30070576 ATACCCTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
TAAATAATATTAGAAATGGCCCATTTTAA
Found at i:30079148 original size:21 final size:20
Alignment explanation
Indices: 30079110--30079149 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
30079100 CTAGGCAAAA
**
30079110 AGTCAATTTATTTTATTCTT
1 AGTCAATTTATTAAATTCTT
30079130 AGTCAAATTTATTAAATTCT
1 AGTC-AATTTATTAAATTCT
30079150 CATTTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (20 bp):
AGTCAATTTATTAAATTCTT
Found at i:30082638 original size:20 final size:20
Alignment explanation
Indices: 30082613--30082651 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30082603 TGATTTTTTA
30082613 TTTGATTCTAATCAAATTGG
1 TTTGATTCTAATCAAATTGG
* *
30082633 TTTGATTTTAATTAAATTG
1 TTTGATTCTAATCAAATTG
30082652 ATTTAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTGATTCTAATCAAATTGG
Found at i:30083137 original size:22 final size:23
Alignment explanation
Indices: 30083099--30083144 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
30083089 ATTCAATTCA
30083099 ATTTATTATATATATATTTGTTT
1 ATTTATTATATATATATTTGTTT
* *
30083122 ATTTA-TATTTATATATTTTTTT
1 ATTTATTATATATATATTTGTTT
30083144 A
1 A
30083145 CTCGCTAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTATTATATATATATTTGTTT
Found at i:30086097 original size:10 final size:9
Alignment explanation
Indices: 30086068--30086093 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30086058 ATTTTATATT
30086068 AATATTTTA
1 AATATTTTA
30086077 AATATTTTA
1 AATATTTTA
30086086 AATATTTT
1 AATATTTT
30086094 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:30089048 original size:41 final size:41
Alignment explanation
Indices: 30088997--30089183 Score: 191
Period size: 41 Copynumber: 4.6 Consensus size: 41
30088987 TTTAAACAAA
* * ** *
30088997 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTAATTCAG
* *
30089038 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * *
30089079 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * * *
30089120 CTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CTTATAG-CCTAATTCAG
*
30089161 TTCACTGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
30089184 ACGTATAGTC
Statistics
Matches: 127, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
40 3 0.02
41 121 0.95
42 3 0.02
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
Found at i:30089211 original size:41 final size:41
Alignment explanation
Indices: 30089038--30089196 Score: 212
Period size: 41 Copynumber: 3.9 Consensus size: 41
30089028 TTTAATTCCG
* * *
30089038 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* * *
30089079 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* *
30089120 CTCACCGGCACTTAGCCTGCTGGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAA
* *
30089161 TTCACTGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
30089197 ATAATTTCAC
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 101 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.28
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
Found at i:30103290 original size:2 final size:2
Alignment explanation
Indices: 30103283--30103307 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30103273 TAGAAATAAA
30103283 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30103308 AATTGCGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30110072 original size:26 final size:24
Alignment explanation
Indices: 30110009--30110079 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 24
30109999 CAATCTTTAT
*
30110009 ATTAAATAATTTTTAATTAAAAATA
1 ATTAAAT-ATTATTAATTAAAAATA
* * *
30110034 A-TAAAAATAATTAGTTATAAAATA
1 ATTAAATATTATTAATTA-AAAATA
30110058 ATTTAAATATTATTAAATTAAA
1 A-TTAAATATTATT-AATTAAA
30110080 TTATAAATTG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
23 8 0.23
24 11 0.31
25 1 0.03
26 11 0.31
27 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
ATTAAATATTATTAATTAAAAATA
Found at i:30114778 original size:15 final size:17
Alignment explanation
Indices: 30114745--30114778 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30114735 ATTAGCTTTA
*
30114745 TTATATATATATGGTTT
1 TTATATATAAATGGTTT
30114762 TTATATATAAAT-GTTT
1 TTATATATAAATGGTTT
30114778 T
1 T
30114779 GTTTCTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
TTATATATAAATGGTTT
Found at i:30119172 original size:16 final size:16
Alignment explanation
Indices: 30119148--30119183 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30119138 TAACCACTTC
* *
30119148 AAAATATAATTAAAAT
1 AAAAAATAAATAAAAT
30119164 AAAAAATAAATAAAAT
1 AAAAAATAAATAAAAT
30119180 AAAA
1 AAAA
30119184 TAAGATTTTT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAATAAATAAAAT
Found at i:30130399 original size:37 final size:37
Alignment explanation
Indices: 30130349--30130439 Score: 173
Period size: 37 Copynumber: 2.5 Consensus size: 37
30130339 ACCAGTTTGG
30130349 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
1 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
*
30130386 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGG
1 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
30130423 CACCCAGTGCCTCATCG
1 CACCCAGTGCCTCATCG
30130440 AATATATCCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.19
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
Found at i:30130478 original size:41 final size:37
Alignment explanation
Indices: 30130349--30130479 Score: 154
Period size: 37 Copynumber: 3.4 Consensus size: 37
30130339 ACCAGTTTGG
**
30130349 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
1 CACCCAGTGCCTCATCGAATAAACCGAAGTAAATTGA
** *
30130386 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGG
1 CACCCAGTGCCTCATCGAATAAACCGAAGTAAATTGA
*
30130423 CACCCAGTGCCTCATCGAATATATCCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAATA-AACCGAAGT-A-AA-TTGA
* *
30130464 CACCCAATGTCTCATC
1 CACCCAGTGCCTCATC
30130480 AACTCGAAGT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
37 55 0.66
38 8 0.10
39 1 0.01
40 2 0.02
41 17 0.20
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGAATAAACCGAAGTAAATTGA
Found at i:30130672 original size:24 final size:24
Alignment explanation
Indices: 30130628--30130673 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
30130618 ATATATACCT
30130628 ATTCAATCAATATAAATTCAATAA
1 ATTCAATCAATATAAATTCAATAA
30130652 ATTC-ATCACATACTAAA-TCAAT
1 ATTCAATCA-ATA-TAAATTCAAT
30130674 TCATTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (24 bp):
ATTCAATCAATATAAATTCAATAA
Found at i:30139754 original size:18 final size:18
Alignment explanation
Indices: 30139731--30139765 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30139721 CAGCCGAATA
30139731 CCATC-ATTCGGCCCAAAG
1 CCATCAATT-GGCCCAAAG
30139749 CCATCAATTGGCCCAAA
1 CCATCAATTGGCCCAAA
30139766 ATTACTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.31, C:0.37, G:0.14, T:0.17
Consensus pattern (18 bp):
CCATCAATTGGCCCAAAG
Found at i:30140031 original size:51 final size:51
Alignment explanation
Indices: 30139955--30140058 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
30139945 CACAAAAATT
*
30139955 ATTAACACCATCAGCACAATAATTTTGACCAAGTGGAAAGCTATTTTGACC
1 ATTAAAACCATCAGCACAATAATTTTGACCAAGTGGAAAGCTATTTTGACC
*
30140006 ATTAAAACCATCAGCACAATGATTTTGACCAAGTGGAAAGCTATTTTGACC
1 ATTAAAACCATCAGCACAATAATTTTGACCAAGTGGAAAGCTATTTTGACC
30140057 AT
1 AT
30140059 AGCCATAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (51 bp):
ATTAAAACCATCAGCACAATAATTTTGACCAAGTGGAAAGCTATTTTGACC
Found at i:30146065 original size:19 final size:20
Alignment explanation
Indices: 30146041--30146084 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
30146031 AAAATTATAC
** *
30146041 TTTTTTAAAATTAATTTATT
1 TTTTTTAAAAAAAATTAATT
30146061 TTTTTTAAAAAAAATTAATT
1 TTTTTTAAAAAAAATTAATT
30146081 TTTT
1 TTTT
30146085 AATGTGTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTAAAAAAAATTAATT
Found at i:30146392 original size:5 final size:5
Alignment explanation
Indices: 30146382--30146407 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30146372 TATAAATTAC
30146382 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
30146408 CAAACTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:30147978 original size:13 final size:13
Alignment explanation
Indices: 30147962--30147986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30147952 TATAAATATT
30147962 ATATATAAAAAAA
1 ATATATAAAAAAA
30147975 ATATATAAAAAA
1 ATATATAAAAAA
30147987 TTAGTTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATATATAAAAAAA
Found at i:30151535 original size:16 final size:17
Alignment explanation
Indices: 30151509--30151542 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30151499 TGAACAAATT
*
30151509 AATTAAAAAATCATAAA
1 AATTAAAAAATAATAAA
30151526 AATT-AAAAATAATAAA
1 AATTAAAAAATAATAAA
30151542 A
1 A
30151543 TCGGTTCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AATTAAAAAATAATAAA
Found at i:30155353 original size:19 final size:20
Alignment explanation
Indices: 30155326--30155372 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
30155316 ATATATAAAA
*
30155326 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTAAAAATTAT
30155346 TTTGAA-TTTTAAAAATTAT
1 TTTGAATTTTTAAAAATTAT
30155365 TTTGAATT
1 TTTGAATT
30155373 ATTTTGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 11 0.46
20 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATTAT
Found at i:30161299 original size:33 final size:33
Alignment explanation
Indices: 30161262--30161327 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
30161252 TGAATTGTCA
* *
30161262 TCTGG-GTTCCTCTTTTGGAATATGTTGTTAGTC
1 TCTGGAGTT-CTCTTCTGGAATATATTGTTAGTC
*
30161295 TCTGGAGTTCTCTTCTGGAATCTATTGTTAGTC
1 TCTGGAGTTCTCTTCTGGAATATATTGTTAGTC
30161328 ATTTTGAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.47
Consensus pattern (33 bp):
TCTGGAGTTCTCTTCTGGAATATATTGTTAGTC
Found at i:30163506 original size:2 final size:2
Alignment explanation
Indices: 30163493--30163522 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30163483 TGGGAGGATC
*
30163493 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30163523 TTTCATCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:30163911 original size:28 final size:31
Alignment explanation
Indices: 30163864--30163928 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
30163854 ACTTTTTATT
* * *
30163864 TTTACACTTTGATCCCAAAA-TTTTGA-ATA
1 TTTACACTTTGAGCCAAAAACTTTTCACATA
30163893 TTTACAC-TTGAGCCAAAAACTTTTCACATA
1 TTTACACTTTGAGCCAAAAACTTTTCACATA
30163923 TTTACA
1 TTTACA
30163929 ATTTAGTCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.32
29 12 0.39
30 9 0.29
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.38
Consensus pattern (31 bp):
TTTACACTTTGAGCCAAAAACTTTTCACATA
Found at i:30163981 original size:3 final size:3
Alignment explanation
Indices: 30163973--30164002 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30163963 CTACTTCTTA
30163973 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30164003 TTAATACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30166008 original size:24 final size:23
Alignment explanation
Indices: 30165971--30166015 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
30165961 AACATTATCA
* *
30165971 AAATAAATATTATAAAGAATATT
1 AAATAAATAATATAAAAAATATT
30165994 AAATAATATAATATAAAAAATA
1 AAATAA-ATAATATAAAAAATA
30166016 GAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATAAATAATATAAAAAATATT
Found at i:30168968 original size:25 final size:22
Alignment explanation
Indices: 30168940--30168985 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
30168930 AACAATAAAA
30168940 ACATATTTTTTATTCTCTAATTTTT
1 ACATA-TTTTTATT-T-TAATTTTT
30168965 ACATATTTTTATTTTAATTTT
1 ACATATTTTTATTTTAATTTT
30168986 CCAACAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 8 0.38
25 5 0.24
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (22 bp):
ACATATTTTTATTTTAATTTTT
Found at i:30169783 original size:10 final size:10
Alignment explanation
Indices: 30169768--30169833 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
30169758 TTTTTTTTAA
30169768 AATTAAAAAT
1 AATTAAAAAT
30169778 AATTAAAAAT
1 AATTAAAAAT
30169788 -ATATAAAAAT
1 AAT-TAAAAAT
*
30169798 AA-CAAAAAT
1 AATTAAAAAT
30169807 -A-TATAAAAT
1 AATTA-AAAAT
30169816 -ATATAAAAATT
1 AAT-TAAAAA-T
30169827 AATTAAA
1 AATTAAA
30169834 TGTTGACATG
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
8 2 0.04
9 14 0.30
10 21 0.45
11 8 0.17
12 2 0.04
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AATTAAAAAT
Found at i:30169823 original size:19 final size:19
Alignment explanation
Indices: 30169771--30169825 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
30169761 TTTTTAAAAT
30169771 TAAAAATAATTAAAAATATA
1 TAAAAATAA-TAAAAATATA
*
30169791 TAAAAATAACAAAAATATA
1 TAAAAATAATAAAAATATA
30169810 T-AAAATATATAAAAAT
1 TAAAAATA-ATAAAAAT
30169826 TAATTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 6 0.19
19 17 0.53
20 9 0.28
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAAATAATAAAAATATA
Found at i:30184733 original size:22 final size:22
Alignment explanation
Indices: 30184708--30184785 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
30184698 CTGACATCCT
30184708 TAAGCTCTCATGTTTAACGTAC
1 TAAGCTCTCATGTTTAACGTAC
*
30184730 TAAGCTCTCATGTTTAACGAAC
1 TAAGCTCTCATGTTTAACGTAC
* * **
30184752 TAAACCCTCATGGCTAACGTAC
1 TAAGCTCTCATGTTTAACGTAC
30184774 TAAGCTCTCATG
1 TAAGCTCTCATG
30184786 CTTTGTATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (22 bp):
TAAGCTCTCATGTTTAACGTAC
Found at i:30195312 original size:20 final size:20
Alignment explanation
Indices: 30195275--30195332 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
30195265 AGTTCCCCCA
*
30195275 AAAAACACATAATGAAATTAG
1 AAAAACATATAAT-AAATTAG
*
30195296 AAAATCATGATAA-AAATTAG
1 AAAAACAT-ATAATAAATTAG
30195316 AAAAACATATAATAAAT
1 AAAAACATATAATAAAT
30195333 AATTCCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.12
20 18 0.56
21 6 0.19
22 4 0.12
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (20 bp):
AAAAACATATAATAAATTAG
Found at i:30197859 original size:43 final size:43
Alignment explanation
Indices: 30197697--30197871 Score: 192
Period size: 43 Copynumber: 4.1 Consensus size: 43
30197687 TTTATGTGAA
* * * *
30197697 AAACACCGCTATAGAACATGACATTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
30197740 AAATGCTGCTAAAGAACATGACCTTTAGCGGCAC-TTTCCCAG
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
30197782 AAATGCCGTTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
30197825 AAACGCCGCTAAATG-TCATGTCCTTTAGCAGCGCTTTTCCCAA
1 AAACGCCGCTAAA-GAACATGACCTTTAGCGGCGCTTTTCCCAC
30197868 AAAC
1 AAAC
30197872 TTGCATTTAA
Statistics
Matches: 110, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 38 0.35
43 71 0.65
44 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:30198736 original size:25 final size:27
Alignment explanation
Indices: 30198695--30198762 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
30198685 AAAAACTTAC
* *
30198695 ACGGCGATG-AGGCAGAGGAG-T-GTCG
1 ACGGCGATGCA-GTAGAGGAGATAGTCA
*
30198720 ACGGCGATGCAGTAGAGGGGATAGTCA
1 ACGGCGATGCAGTAGAGGAGATAGTCA
*
30198747 ACGGTGATGCAGTAGA
1 ACGGCGATGCAGTAGA
30198763 CGGTCAGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 16 0.44
26 2 0.06
27 18 0.50
ACGTcount: A:0.28, C:0.15, G:0.43, T:0.15
Consensus pattern (27 bp):
ACGGCGATGCAGTAGAGGAGATAGTCA
Found at i:30198808 original size:14 final size:14
Alignment explanation
Indices: 30198789--30198833 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
30198779 AAGGGATTTT
*
30198789 GGATTTTGATTTGG
1 GGATTTCGATTTGG
*
30198803 GGATTTCGATGTGG
1 GGATTTCGATTTGG
30198817 GGATTTCGATTTGG
1 GGATTTCGATTTGG
30198831 GGA
1 GGA
30198834 AAATTAAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.16, C:0.04, G:0.40, T:0.40
Consensus pattern (14 bp):
GGATTTCGATTTGG
Found at i:30198911 original size:28 final size:29
Alignment explanation
Indices: 30198861--30198919 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
30198851 GGTTTCAATT
* **
30198861 TTTAGGGGTGAAAATAAGGGATTTTAGGG
1 TTTAGGGATGAAAATAAAAGATTTTAGGG
*
30198890 TTTAGGGAT-AAAATAAAAGATTTTGGGG
1 TTTAGGGATGAAAATAAAAGATTTTAGGG
30198918 TT
1 TT
30198920 ATGGTTTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (29 bp):
TTTAGGGATGAAAATAAAAGATTTTAGGG
Found at i:30199462 original size:2 final size:2
Alignment explanation
Indices: 30199457--30199481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30199447 TCTAAAAAAC
30199457 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30199482 TAATATTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30200708 original size:14 final size:14
Alignment explanation
Indices: 30200691--30200719 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30200681 AGGGTTAGGG
30200691 TTAAGGTTTGAAGT
1 TTAAGGTTTGAAGT
30200705 TTAAGGTTTGAAGT
1 TTAAGGTTTGAAGT
30200719 T
1 T
30200720 CATGGTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (14 bp):
TTAAGGTTTGAAGT
Found at i:30200726 original size:14 final size:14
Alignment explanation
Indices: 30200693--30200726 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30200683 GGTTAGGGTT
*
30200693 AAGGTTTGAAGTTT
1 AAGGTTTGAAGTTC
30200707 AAGGTTTGAAGTTC
1 AAGGTTTGAAGTTC
*
30200721 ATGGTT
1 AAGGTT
30200727 CAAGGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.41
Consensus pattern (14 bp):
AAGGTTTGAAGTTC
Found at i:30202946 original size:14 final size:15
Alignment explanation
Indices: 30202921--30202951 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30202911 GATAAAAAAT
30202921 AAATATTGGTTTTTA
1 AAATATTGGTTTTTA
*
30202936 AAATATTGTTTTTTA
1 AAATATTGGTTTTTA
30202951 A
1 A
30202952 TTTTAGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
AAATATTGGTTTTTA
Found at i:30203143 original size:21 final size:21
Alignment explanation
Indices: 30203089--30203149 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
30203079 TCAAAATTTT
*
30203089 ATATTAAATA-AAAATTTAAA
1 ATATTAAATATTAAATTTAAA
* *
30203109 ATAATTATCA-ATTATATTTAAA
1 AT-ATTA-AATATTAAATTTAAA
30203131 ATATTAAATATTAAGATTT
1 ATATTAAATATTAA-ATTT
30203150 TCATTTCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
20 3 0.10
21 13 0.42
22 15 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATTAAATATTAAATTTAAA
Found at i:30209082 original size:5 final size:5
Alignment explanation
Indices: 30209067--30209109 Score: 68
Period size: 5 Copynumber: 8.2 Consensus size: 5
30209057 TTTAAAAGAA
30209067 TATATT TATAT TATAT TATAT TATAT TATAT TATAT TAATAT T
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT T-ATAT T
30209110 TAATAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 27 0.75
6 9 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:30210201 original size:45 final size:45
Alignment explanation
Indices: 30210148--30210335 Score: 170
Period size: 45 Copynumber: 4.2 Consensus size: 45
30210138 TATCTGCAAA
* *
30210148 ATTTGTTGTGTATCCACAGCCAAAGGCAGATTCCATTTACGGGTT
1 ATTTGTTGTGTATCCACAGCCAGAGGCAGATTCCATTTACGAGTT
* *
30210193 ATTTGTTGTGTATCCACATG-CAGAGGCAAATTCCATCTACGAGTT
1 ATTTGTTGTGTATCCACA-GCCAGAGGCAGATTCCATTTACGAGTT
* * * * * * *
30210238 ATTTGCTATGTAATCCACAACCAGAGGTAGATTTCATTTGCAAG--
1 ATTTGTTGTGT-ATCCACAGCCAGAGGCAGATTCCATTTACGAGTT
* * * *
30210282 ACTTTGTTGTGTA-CCAACAGCCAGAGACAGATTCCATCTGCGAGAT
1 A-TTTGTTGTGTATCC-ACAGCCAGAGGCAGATTCCATTTACGAGTT
30210328 -TTTGTTGT
1 ATTTGTTGT
30210336 ATGTCCATAG
Statistics
Matches: 115, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
43 2 0.02
44 32 0.28
45 56 0.49
46 25 0.22
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (45 bp):
ATTTGTTGTGTATCCACAGCCAGAGGCAGATTCCATTTACGAGTT
Found at i:30211345 original size:19 final size:18
Alignment explanation
Indices: 30211308--30211350 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
30211298 ACCAAAAAAT
** *
30211308 ATTTTAAATTCATTTTTG
1 ATTTTAAATAAATTATTG
30211326 AGTTTTAAATAAATTATTG
1 A-TTTTAAATAAATTATTG
30211345 ATTTTA
1 ATTTTA
30211351 GTTTAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (18 bp):
ATTTTAAATAAATTATTG
Found at i:30217166 original size:45 final size:45
Alignment explanation
Indices: 30217107--30217194 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
30217097 TCATACATGC
* * * *
30217107 GGATTCATAGAAGAAACTTCATGGATATAGCAGATTCAAACATAA
1 GGATACATAAAAGAAACTTCATGAACATAGCAGATTCAAACATAA
*
30217152 GGATACATAAAAGAAACTTCATGAACATAGCAGATTCATACAT
1 GGATACATAAAAGAAACTTCATGAACATAGCAGATTCAAACAT
30217195 GCGGACTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (45 bp):
GGATACATAAAAGAAACTTCATGAACATAGCAGATTCAAACATAA
Found at i:30224670 original size:5 final size:5
Alignment explanation
Indices: 30224660--30224687 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
30224650 TATCTCTTTA
30224660 TTAAT TTAAT TTAAT TTAAT TTAAT TTA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTA
30224688 TTAGAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:30226435 original size:42 final size:42
Alignment explanation
Indices: 30226363--30226549 Score: 193
Period size: 42 Copynumber: 4.4 Consensus size: 42
30226353 ACGTCTCTAA
* *
30226363 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-TG-AAAAAACGCCGCTAAAGATCATGTT
*
30226407 CTTTAGCAGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
* *
30226449 CTTTAGCGGCGCTT-TGGAAGAAAATGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAT-GAA-AAAACGCCGCTAAAGA-TCATGTT
* * ** *
30226492 CTATAGCGGCGCTTGTTCAAAAATGCCGCTAATAG-T-AGTGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAA-AGATCA-TGTT
30226534 CTTTAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
30226550 TTCACAAATG
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
41 2 0.02
42 74 0.59
43 35 0.28
44 14 0.11
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
Found at i:30226491 original size:85 final size:85
Alignment explanation
Indices: 30226384--30226547 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
30226374 CTTACAGAAA
* *
30226384 AAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTATGAAAAAACGCCGCTAA-AGATCA-TG
1 AAAACGCCGCTAAAGATAATGTTCTATAGCAGCGCTTATGAAAAAACGCCGCTAATAG-T-AGTG
30226447 TTCTTTAGCGGCGCTTTGGAAG
64 TTCTTTAGCGGCGCTTTGGAAG
* * * ** *
30226469 AAAATGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTGTTCAAAAATGCCGCTAATAGTAGTGT
1 AAAACGCCGCTAAAGA-TAATGTTCTATAGCAGCGCTTATGAAAAAACGCCGCTAATAGTAGTGT
30226533 TCTTTAGCGGCGCTT
65 TCTTTAGCGGCGCTT
30226548 ATTTCACAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 2 0.03
85 64 0.94
86 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (85 bp):
AAAACGCCGCTAAAGATAATGTTCTATAGCAGCGCTTATGAAAAAACGCCGCTAATAGTAGTGTT
CTTTAGCGGCGCTTTGGAAG
Found at i:30227010 original size:21 final size:21
Alignment explanation
Indices: 30226986--30227075 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 21
30226976 GCTTCTATCG
* *
30226986 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
30227007 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
30227028 TTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
30227049 CTGCTTCCCTCGCTACCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
30227070 CTGCTT
1 CTGCTT
30227076 TAAGTTGTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:30228611 original size:9 final size:9
Alignment explanation
Indices: 30228590--30229119 Score: 551
Period size: 9 Copynumber: 58.2 Consensus size: 9
30228580 NNNNNNNNNN
*
30228590 TTATGTAGG
1 TTATGTAAG
* *
30228599 TTATTTAAT
1 TTATGTAAG
30228608 TTATGTAAG
1 TTATGTAAG
30228617 TTATGTAAG
1 TTATGTAAG
* *
30228626 TTATTTAAT
1 TTATGTAAG
*
30228635 TTATGTAGG
1 TTATGTAAG
30228644 TTATGTAAG
1 TTATGTAAG
30228653 TTATGTAAG
1 TTATGTAAG
30228662 TTATGTAAG
1 TTATGTAAG
* *
30228671 TTATTTAAT
1 TTATGTAAG
*
30228680 TTATGTAGGG
1 TTATGTA-AG
30228690 TTATGTAAG
1 TTATGTAAG
* **
30228699 TTATTTATT
1 TTATGTAAG
* *
30228708 TTATGCAGGG
1 TTATGTA-AG
30228718 TTATGTAAG
1 TTATGTAAG
*
30228727 TTATGTAAT
1 TTATGTAAG
*
30228736 TTATGCAAG
1 TTATGTAAG
30228745 TTTATGTAAG
1 -TTATGTAAG
30228755 TTATGTAAG
1 TTATGTAAG
*
30228764 TTATGTAAT
1 TTATGTAAG
*
30228773 TTATGCAAG
1 TTATGTAAG
30228782 TTTATGTAAG
1 -TTATGTAAG
30228792 TTATGTAAG
1 TTATGTAAG
* *
30228801 TTATTTAAT
1 TTATGTAAG
30228810 TTATGTAAG
1 TTATGTAAG
30228819 TTATGTAAG
1 TTATGTAAG
* *
30228828 TTATTTAAT
1 TTATGTAAG
*
30228837 TTATGCAAG
1 TTATGTAAG
30228846 TTATGTAAG
1 TTATGTAAG
* * *
30228855 TTGTTTAAT
1 TTATGTAAG
30228864 TTATGTAAG
1 TTATGTAAG
30228873 TTATGTAAG
1 TTATGTAAG
*
30228882 TTATGTAAT
1 TTATGTAAG
*
30228891 TTATGCAAG
1 TTATGTAAG
30228900 TTTATGTAAG
1 -TTATGTAAG
30228910 TTATGTAAG
1 TTATGTAAG
*
30228919 TTACT-TAAT
1 TTA-TGTAAG
30228928 TTATGTAAG
1 TTATGTAAG
30228937 TTATGTAAG
1 TTATGTAAG
* *
30228946 TTATTTAAT
1 TTATGTAAG
30228955 TTATGTAAG
1 TTATGTAAG
30228964 TTATGTAAG
1 TTATGTAAG
* *
30228973 TTATTTAAT
1 TTATGTAAG
*
30228982 TTACT-TAAT
1 TTA-TGTAAG
30228991 TTATGTAAG
1 TTATGTAAG
* *
30229000 TTATTTAAT
1 TTATGTAAG
*
30229009 TTATGTAGG
1 TTATGTAAG
30229018 TTATGTAAG
1 TTATGTAAG
* *
30229027 TTATTTAAT
1 TTATGTAAG
**
30229036 TTATGTCGG
1 TTATGTAAG
30229045 TTATGTAAG
1 TTATGTAAG
30229054 TTATGTAAG
1 TTATGTAAG
* *
30229063 TTATTTAAT
1 TTATGTAAG
*
30229072 TTATGCAAG
1 TTATGTAAG
30229081 TTTATGTAAG
1 -TTATGTAAG
30229091 TTATGTAAG
1 TTATGTAAG
*
30229100 TTTTGTAAG
1 TTATGTAAG
* *
30229109 ATATGTGAG
1 TTATGTAAG
30229118 TT
1 TT
30229120 TCTATATATG
Statistics
Matches: 423, Mismatches: 88, Indels: 20
0.80 0.17 0.04
Matches are distributed among these distances:
8 2 0.00
9 374 0.88
10 47 0.11
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:30229161 original size:8 final size:8
Alignment explanation
Indices: 30229148--30229200 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
30229138 TTGTATGTTA
30229148 GTTATTAT
1 GTTATTAT
30229156 GTTATTAT
1 GTTATTAT
30229164 GTTAATATAT
1 GTT-AT-TAT
*
30229174 AAGTTATTTAA
1 --GTTA-TTAT
30229185 GTTATTAT
1 GTTATTAT
30229193 GTTATTAT
1 GTTATTAT
30229201 ATAAAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 22 0.58
9 6 0.16
10 3 0.08
11 3 0.08
12 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (8 bp):
GTTATTAT
Found at i:30229188 original size:29 final size:29
Alignment explanation
Indices: 30229147--30229253 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 29
30229137 ATTGTATGTT
*
30229147 AGTTAT-TATGTTATTATGTTAATATATA
1 AGTTATGTAAGTTATTATGTTAATATATA
* *
30229175 AGTTATTTAAGTTATTATGTTATTATATAA
1 AGTTATGTAAGTTATTATGTTAATATAT-A
* *
30229205 AGTATTATGTAATTTATTATGTTATTATATGTA
1 AG--TTATGTAAGTTATTATGTTA--ATATATA
30229238 AGTTATGTAAGTTATT
1 AGTTATGTAAGTTATT
30229254 TAATTTATGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.09
29 19 0.29
30 3 0.05
31 13 0.20
32 18 0.27
33 3 0.05
34 4 0.06
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (29 bp):
AGTTATGTAAGTTATTATGTTAATATATA
Found at i:30229220 original size:37 final size:37
Alignment explanation
Indices: 30229147--30229220 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
30229137 ATTGTATGTT
* * *
30229147 AGTTATTATGTTATTATGTTAATATATAAGTTATTTA
1 AGTTATTATGTTATTATATAAATATATAAGTAATTTA
*
30229184 AGTTATTATGTTATTATATAAAGTAT-TATGTAATTTA
1 AGTTATTATGTTATTATATAAA-TATATAAGTAATTTA
30229221 TTATGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 29 0.91
38 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (37 bp):
AGTTATTATGTTATTATATAAATATATAAGTAATTTA
Found at i:30229227 original size:32 final size:29
Alignment explanation
Indices: 30229147--30229253 Score: 126
Period size: 32 Copynumber: 3.6 Consensus size: 29
30229137 ATTGTATGTT
* *
30229147 AGTTAT-TATGTTATTATGTTAATATATA
1 AGTTATGTAAGTTATTATGTTATTATATA
*
30229175 AGTTATTTAAGTTATTATGTTATTATATAA
1 AGTTATGTAAGTTATTATGTTATTATAT-A
*
30229205 AGTATTATGTAATTTATTATGTTATTATATGTA
1 AG--TTATGTAAGTTATTATGTTATTATA--TA
30229238 AGTTATGTAAGTTATT
1 AGTTATGTAAGTTATT
30229254 TAATTTATGT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.09
29 19 0.28
30 3 0.04
31 13 0.19
32 23 0.34
33 3 0.04
34 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (29 bp):
AGTTATGTAAGTTATTATGTTATTATATA
Found at i:30229230 original size:20 final size:20
Alignment explanation
Indices: 30229157--30229270 Score: 74
Period size: 21 Copynumber: 5.6 Consensus size: 20
30229147 AGTTATTATG
* * * *
30229157 TTATTATGTTAATATATAAG
1 TTATTAAGTTATTATGTAAT
*
30229177 TTATTTAAGTTATTATGTTAT
1 TTA-TTAAGTTATTATGTAAT
*
30229198 TATATAAAG-TATTATGTAAT
1 T-TATTAAGTTATTATGTAAT
* *
30229218 TTATTATGTTATTATATGTAAG
1 TTATTAAGTTA-T-TATGTAAT
30229240 TTATGTAAGTTA-T-T-TAAT
1 TTAT-TAAGTTATTATGTAAT
30229258 TTATGTAAGTTAT
1 TTAT-TAAGTTAT
30229271 GCAAGCTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
18 15 0.20
19 6 0.08
20 17 0.23
21 18 0.24
22 13 0.17
23 6 0.08
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (20 bp):
TTATTAAGTTATTATGTAAT
Found at i:30229238 original size:22 final size:23
Alignment explanation
Indices: 30229210--30229280 Score: 63
Period size: 27 Copynumber: 2.9 Consensus size: 23
30229200 TATAAAGTAT
* *
30229210 TATGTAATTTAT-TATGTTATTA
1 TATGTAAGTTATGTAAGTTATTA
30229232 TATGTAAGTTATGTAAGTTATTTAA
1 TATGTAAGTTATGTAAGTTA-TT-A
*
30229257 TTTATGTAAGTTATGCAAGCTTAT
1 --TATGTAAGTTATGTAAG-TTAT
30229281 ATAACAGTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
24 2 0.05
25 1 0.03
27 17 0.43
28 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (23 bp):
TATGTAAGTTATGTAAGTTATTA
Found at i:30229246 original size:9 final size:9
Alignment explanation
Indices: 30229232--30229294 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
30229222 TATGTTATTA
30229232 TATGTAAGT
1 TATGTAAGT
30229241 TATGTAAGT
1 TATGTAAGT
* *
30229250 TATTTAATT
1 TATGTAAGT
30229259 TATGTAAGT
1 TATGTAAGT
*
30229268 TATGCAAGCT
1 TATGTAAG-T
*
30229278 TATATAACAGT
1 TATGT-A-AGT
30229289 TATGTA
1 TATGTA
30229295 TTACAACATA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
9 30 0.70
10 5 0.12
11 6 0.14
12 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:30229531 original size:15 final size:15
Alignment explanation
Indices: 30229511--30229551 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
30229501 GAAAATGAAG
*
30229511 TAAATTTAATACTAA
1 TAAATTTAATACAAA
30229526 TAAATTTTAATACAAA
1 TAAA-TTTAATACAAA
30229542 TAAATTTAAT
1 TAAATTTAAT
30229552 TAAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTTAATACAAA
Found at i:30229603 original size:19 final size:17
Alignment explanation
Indices: 30229558--30229590 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30229548 TAATTAAATT
30229558 ATTTAGAAAACTTATAA
1 ATTTAGAAAACTTATAA
30229575 ATTTAGAAAACTTATA
1 ATTTAGAAAACTTATA
30229591 TAGATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTTAGAAAACTTATAA
Found at i:30230811 original size:219 final size:219
Alignment explanation
Indices: 30230424--30230832 Score: 678
Period size: 219 Copynumber: 1.9 Consensus size: 219
30230414 CATACTTTGA
* * *
30230424 AAACAGTACCAAATGAGTTCAACACATAAACAGTAACAAAGCATGTGTTCTGTACCTTCAGAATG
1 AAACAGTACCAAATGAGTTCAACAAATAAACAGTAACAAAGCATGTGTTCTGTACCTTAAGAACG
* *
30230489 ATGACGAAAACTGAAATTAAAGCAATGAAATGGATTGACCAAAATCTGGAGAAGAAAAAAAAAAG
66 ATGAAGAAAACTGAAATTAAAGCAATGAAATGGATTGACCAAAAACTGGAGAAGAAAAAAAAAAG
* * *
30230554 TTAAAATCAGTTCCTAACAAATTAAACCGCAGACAAAAACAGTAATGAACAATAGAAGCAGTACC
131 TTAAAATCAGTTCCTAACAAACTAAACCACACACAAAAACAGTAATGAACAATAGAAGCAGTACC
30230619 AAATTGACTGAAAATAACCATGTC
196 AAATTGACTGAAAATAACCATGTC
30230643 AAACAGTACCAAATGAGTTCAACAAATAAACAGTAACAAAGCATGTGTTCTGTACCTTAAGAACG
1 AAACAGTACCAAATGAGTTCAACAAATAAACAGTAACAAAGCATGTGTTCTGTACCTTAAGAACG
30230708 ATGAAGAAAACTGAAATTAAAGCAATGAAATGGATTGACCAAAAACTGGAGAA-AAAAAACAAAA
66 ATGAAGAAAACTGAAATTAAAGCAATGAAATGGATTGACCAAAAACTGGAGAAGAAAAAA-AAAA
** **
30230772 GTTAAACA-CAGTTCCTAACACCCTAAACCATTCACAAAAACAGTAATGAACAATAGAAGCA
130 GTTAAA-ATCAGTTCCTAACAAACTAAACCACACACAAAAACAGTAATGAACAATAGAAGCA
30230833 ATAACTAACC
Statistics
Matches: 176, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
218 6 0.03
219 169 0.96
220 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (219 bp):
AAACAGTACCAAATGAGTTCAACAAATAAACAGTAACAAAGCATGTGTTCTGTACCTTAAGAACG
ATGAAGAAAACTGAAATTAAAGCAATGAAATGGATTGACCAAAAACTGGAGAAGAAAAAAAAAAG
TTAAAATCAGTTCCTAACAAACTAAACCACACACAAAAACAGTAATGAACAATAGAAGCAGTACC
AAATTGACTGAAAATAACCATGTC
Found at i:30234456 original size:227 final size:224
Alignment explanation
Indices: 30233931--30234570 Score: 1089
Period size: 227 Copynumber: 2.9 Consensus size: 224
30233921 AACGAAGCCG
*
30233931 TTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCCGCTAATATTGTTCTTTAGCGGCGTTT
1 TTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGTTT
*
30233996 TATCGTAAATGCCACTAATTCTAATATACCTCAAAACTAAACGCTGCGTTTTGGTTAAGGTATTT
66 TATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTT
*
30234061 TGCGGC-ACTTACAAATAAACGCCACTAATGATGTTCTTTTATGGCG-TTTTTAATAA-G---C-
131 TGCGGCGA-TTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTAATAACGCCACT
* *
30234119 -ACCAATCTACCTCAGGACCAAACGGTGCG
195 AACCAATCTACCTCAAGACCAAACGGTGCA
* *
30234148 TTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCAGCTAATACTATTCTTTAGCGGCGTTT
1 TTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGTTT
*
30234213 TATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTT
66 TATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTT
30234278 TGCGGCGATTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTAATAAGCGCCACT
131 TGCGGCGATTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTAATAA-CGCCACT
30234343 AACACTAATCTACCTCAAGACCAAACGGTGCA
195 AAC-C-AATCTACCTCAAGACCAAACGGTGCA
*
30234375 TTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCATTT
1 TTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGTTT
30234440 TATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTT
66 TATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTT
*
30234505 TGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTTAATAACGCCACT
131 TGCGGCGATTACAAATAAACGCCACTAATGATGTTCTTTTACGGCG-TTTTTTAATAACGCCACT
30234570 A
195 A
30234571 GTTGTTCGGG
Statistics
Matches: 398, Mismatches: 13, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
217 168 0.42
218 11 0.03
220 1 0.00
223 1 0.00
225 2 0.01
226 1 0.00
227 203 0.51
228 11 0.03
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (224 bp):
TTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGTTT
TATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTT
TGCGGCGATTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTAATAACGCCACTA
ACCAATCTACCTCAAGACCAAACGGTGCA
Done.