Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 76 of 135
Found at i:29771017 original size:62 final size:62
Alignment explanation
Indices: 29770951--29771130 Score: 360
Period size: 62 Copynumber: 2.9 Consensus size: 62
29770941 TAAATAAAGA
29770951 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
1 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
29771013 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
1 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
29771075 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAA
1 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAA
29771131 TTAGTTCAAG
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 118 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (62 bp):
TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
Found at i:29790762 original size:24 final size:24
Alignment explanation
Indices: 29790728--29790799 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
29790718 TCGTTTTGTG
*
29790728 GCAAAGAATGAATTGACGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
29790752 GCAAAGGATGAATTGACGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
*
29790776 GCAAAGGATGAATTGACGGCAAAT
1 GCAAAGGATGAATTGACGGTAAAT
29790800 TACCCAAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.19
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGTAAAT
Found at i:29790901 original size:21 final size:21
Alignment explanation
Indices: 29790876--29790939 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
29790866 TGAGCTTCTA
29790876 TTAACTCATATGAGTTTCCGT
1 TTAACTCATATGAGTTTCCGT
* * *
29790897 TTAAC-CCTAATGGGTTCCCGT
1 TTAACTCAT-ATGAGTTTCCGT
* * *
29790918 TTAGCTCTTATGAGCTTCCGT
1 TTAACTCATATGAGTTTCCGT
29790939 T
1 T
29790940 CAACCTTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (21 bp):
TTAACTCATATGAGTTTCCGT
Found at i:29790997 original size:19 final size:21
Alignment explanation
Indices: 29790954--29790998 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29790944 CTTTATAAGT
* *
29790954 TTCTGTTTAGCACTTATGTGC
1 TTCTGTTTAGCACTTACGGGC
29790975 TTCTGTTTAGC-CTT-CGGGC
1 TTCTGTTTAGCACTTACGGGC
29790994 TTCTG
1 TTCTG
29790999 AAAACGATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 3 0.14
21 11 0.50
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (21 bp):
TTCTGTTTAGCACTTACGGGC
Found at i:29794226 original size:18 final size:18
Alignment explanation
Indices: 29794205--29794249 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29794195 TTTGAAAAGT
*
29794205 TATTAAATATTTAAA-AAA
1 TATTAAA-ATTAAAATAAA
29794223 TATTAAAATTAAAATAAA
1 TATTAAAATTAAAATAAA
*
29794241 TATAAAAAT
1 TATTAAAAT
29794250 AATATCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATTAAAATTAAAATAAA
Found at i:29794757 original size:29 final size:30
Alignment explanation
Indices: 29794690--29794758 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
29794680 TTAATTTAAT
* *
29794690 TTAATTTAATTGTTTTGAATAATATAATGA
1 TTAATTTAATTGTTTTGAATAATAAAAAGA
* * *
29794720 TAAAATTAATT-TATTT-AATAATAAAAAGG
1 TTAATTTAATTGT-TTTGAATAATAAAAAGA
29794749 TTAATTTAAT
1 TTAATTTAAT
29794759 CATGTCCCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TTAATTTAATTGTTTTGAATAATAAAAAGA
Found at i:29805074 original size:15 final size:15
Alignment explanation
Indices: 29805056--29805089 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29805046 TATTAAATTA
29805056 TTTAAAATTAATTTT
1 TTTAAAATTAATTTT
* *
29805071 TTTAATATTGATTTT
1 TTTAAAATTAATTTT
29805086 TTTA
1 TTTA
29805090 TTGATCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTAAAATTAATTTT
Found at i:29808832 original size:44 final size:44
Alignment explanation
Indices: 29808783--29808956 Score: 348
Period size: 44 Copynumber: 4.0 Consensus size: 44
29808773 TCAATCGGAC
29808783 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
1 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
29808827 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
1 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
29808871 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
1 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
29808915 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAG
1 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAG
29808957 ATTAAGAGTC
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 130 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (44 bp):
TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
Found at i:29810231 original size:14 final size:14
Alignment explanation
Indices: 29810212--29810238 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29810202 TTGATAATTG
29810212 AAAAATAATTATTA
1 AAAAATAATTATTA
29810226 AAAAATAATTATT
1 AAAAATAATTATT
29810239 GAATTTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATAATTATTA
Found at i:29810939 original size:21 final size:21
Alignment explanation
Indices: 29810915--29810959 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29810905 AAAAAATTAT
* *
29810915 AAAATTTTATAAAATCGT-AAG
1 AAAATTATACAAAAT-GTAAAG
29810936 AAAATTATACAAAATGTAAAG
1 AAAATTATACAAAATGTAAAG
29810957 AAA
1 AAA
29810960 TATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTATACAAAATGTAAAG
Found at i:29811205 original size:19 final size:18
Alignment explanation
Indices: 29811177--29811223 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
29811167 ATTTATGTTT
29811177 TTTATAATTTTAT-TAAAA
1 TTTATAATTTT-TCTAAAA
29811195 TTTAGTAATTTTTCTAAAA
1 TTTA-TAATTTTTCTAAAA
*
29811214 TTTATTATTT
1 TTTATAATTT
29811224 ATGATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTATAATTTTTCTAAAA
Found at i:29811206 original size:27 final size:29
Alignment explanation
Indices: 29811146--29811206 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
29811136 TTTTTATAAA
*
29811146 AATTTTCTAATTTTTAATAAAATTTATGT
1 AATTTTATAATTTTTAATAAAATTTATGT
* *
29811175 -TTTTTATAA-TTTTATTAAAATTTA-GT
1 AATTTTATAATTTTTAATAAAATTTATGT
29811201 AATTTT
1 AATTTT
29811207 TCTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 18 0.67
28 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AATTTTATAATTTTTAATAAAATTTATGT
Found at i:29811231 original size:47 final size:48
Alignment explanation
Indices: 29811128--29811234 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 48
29811118 TTGTTAATTT
*
29811128 TTTTATGAT--TTTTATAAAAATTTTCTAATTTTTAATAAAATTTATG
1 TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
* * * *
29811174 TTTT-TTATAATTTTATTAAAATTTAGTAATTTTT-CTAAAATTTAT-
1 TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
29811219 TATTTATGATAATTTT
1 T-TTTATGATAATTTT
29811235 TTTCTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 4 0.08
46 17 0.33
47 30 0.59
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (48 bp):
TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
Found at i:29811749 original size:89 final size:90
Alignment explanation
Indices: 29811616--29811789 Score: 230
Period size: 89 Copynumber: 1.9 Consensus size: 90
29811606 GTTCCTTTTT
* ** *
29811616 TTTTTTTACACTCAATTTGGGTACTTGAGTTTTTAAAATATATCAAAAAGACCCTCAAA-TCTTT
1 TTTTTTTACACTCAATTTGGGTACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACT-TTT
29811680 TCA-AAAAAAGCAATCAAGCCCCTTAC
65 TCATAAAAAA-CAATCAAGCCCCTTAC
* *
29811706 TTTTTTTGCACTCAA-TTGGGTACTTAAACTTTCAAAA-AGTATCAAAAAGATCCTCAAACTTTT
1 TTTTTTTACACTCAATTTGGGTACTTAAACTTTCAAAATA-TATCAAAAAGACCCTCAAACTTTT
*
29811769 TCATAAAAAACAATTAAGCCC
65 TCATAAAAAACAATCAAGCCC
29811790 ATGCATTTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
88 1 0.01
89 52 0.70
90 21 0.28
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (90 bp):
TTTTTTTACACTCAATTTGGGTACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTTTTT
CATAAAAAACAATCAAGCCCCTTAC
Found at i:29811824 original size:7 final size:7
Alignment explanation
Indices: 29811798--29811840 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
29811788 CCATGCATTT
29811798 ATTAAAA
1 ATTAAAA
29811805 ATTATAAA
1 ATTA-AAA
29811813 A--AAAA
1 ATTAAAA
29811818 ATTAAAA
1 ATTAAAA
29811825 TATTAAAA
1 -ATTAAAA
29811833 ATTAAAA
1 ATTAAAA
29811840 A
1 A
29811841 ATATATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.12
6 1 0.03
7 16 0.50
8 11 0.34
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATTAAAA
Found at i:29811849 original size:18 final size:19
Alignment explanation
Indices: 29811821--29811871 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
29811811 AAAAAAAATT
29811821 AAAATAT-TAAAAAT-TAA
1 AAAATATATAAAAATATAA
29811838 AAAATATATAAAAATCATAA
1 AAAATATATAAAAAT-ATAA
* *
29811858 TAATTATATAAAAA
1 AAAATATATAAAAA
29811872 ATTGTACATN
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
20 15 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATATATAAAAATATAA
Found at i:29811961 original size:21 final size:21
Alignment explanation
Indices: 29811937--29811981 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29811927 AAAAAATTAT
* *
29811937 AAAATTTTATAAAATCGT-AAG
1 AAAATTATACAAAAT-GTAAAG
29811958 AAAATTATACAAAATGTAAAG
1 AAAATTATACAAAATGTAAAG
29811979 AAA
1 AAA
29811982 TATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTATACAAAATGTAAAG
Found at i:29812227 original size:19 final size:18
Alignment explanation
Indices: 29812199--29812245 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
29812189 ATTTATGTTT
29812199 TTTATAATTTTAT-TAAAA
1 TTTATAATTTT-TCTAAAA
29812217 TTTAGTAATTTTTCTAAAA
1 TTTA-TAATTTTTCTAAAA
*
29812236 TTTATTATTT
1 TTTATAATTT
29812246 ATGATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTATAATTTTTCTAAAA
Found at i:29812228 original size:27 final size:29
Alignment explanation
Indices: 29812168--29812228 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
29812158 TTTTTATAAA
*
29812168 AATTTTCTAATTTTTAATAAAATTTATGT
1 AATTTTATAATTTTTAATAAAATTTATGT
* *
29812197 -TTTTTATAA-TTTTATTAAAATTTA-GT
1 AATTTTATAATTTTTAATAAAATTTATGT
29812223 AATTTT
1 AATTTT
29812229 TCTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 18 0.67
28 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AATTTTATAATTTTTAATAAAATTTATGT
Found at i:29812253 original size:47 final size:48
Alignment explanation
Indices: 29812150--29812256 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 48
29812140 TTGTTAATTT
*
29812150 TTTTATGAT--TTTTATAAAAATTTTCTAATTTTTAATAAAATTTATG
1 TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
* * * *
29812196 TTTT-TTATAATTTTATTAAAATTTAGTAATTTTT-CTAAAATTTAT-
1 TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
29812241 TATTTATGATAATTTT
1 T-TTTATGATAATTTT
29812257 TTTCTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 4 0.08
46 17 0.33
47 30 0.59
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (48 bp):
TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
Found at i:29812800 original size:121 final size:121
Alignment explanation
Indices: 29812645--29812899 Score: 343
Period size: 129 Copynumber: 2.1 Consensus size: 121
29812635 AGAATTTGTG
* * *
29812645 TTTTT-TTTTGTTTAAGTTAGACTTTAAATTTGACAATTGTTCTCACATTAGGGTTTATA-ATTT
1 TTTTTGTTTTGTCTAAGTTAGACTTTAAATGTGACAATTGTTCTCACATTACGGTTTATATATTT
*
29812708 TTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGGGCTTGTACTT
66 TTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
*
29812764 TTTTTGTTGTTGTCTAAGTTAGACTTTAAATGTGACAATTGTTGTCACATTACGGTTTATACTCT
1 TTTTTGTT-TTGTCTAAGTTAGACTTTAAATGTGACAATTGTTCTCACATTACGGTTTATA----
* * * *
29812829 TTTTTTTTTTTTTCTATATTAGGCCTTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
61 ---TATTTTTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
29812893 TTTTTGT
1 TTTTTGT
29812900 CAAAGTTAGG
Statistics
Matches: 117, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
119 5 0.04
120 2 0.02
121 48 0.41
129 62 0.53
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (121 bp):
TTTTTGTTTTGTCTAAGTTAGACTTTAAATGTGACAATTGTTCTCACATTACGGTTTATATATTT
TTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
Found at i:29812803 original size:64 final size:64
Alignment explanation
Indices: 29812731--29812899 Score: 162
Period size: 65 Copynumber: 2.6 Consensus size: 64
29812721 GGCCCTAGGC
*
29812731 TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGTTGTTGTCTA-AGTTAGACTTTA-AA
1 TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGTTGTTGTCTATA-TTAGACCTTAGAA
* * * ** * * * * * * *
29812794 TGTGACAATTGTTGTCACATTACGGTTTATACTCTTTTTTTTTTTTTTCTATATTAGGCCTTAGG
1 T-TGACAATTATTCTAACATTGGGGCTTGTACT-TTTTTTGTTGTTGTCTATATTAGACCTTAGA
*
29812859 C
64 A
*
29812860 TTGACAATTATTCTAACATTGGAGCTTGTACTTTTTTTGT
1 TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGT
29812900 CAAAGTTAGG
Statistics
Matches: 79, Mismatches: 23, Indels: 7
0.72 0.21 0.06
Matches are distributed among these distances:
63 1 0.01
64 31 0.39
65 45 0.57
66 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (64 bp):
TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGTTGTTGTCTATATTAGACCTTAGAA
Found at i:29812879 original size:65 final size:63
Alignment explanation
Indices: 29812705--29812897 Score: 165
Period size: 64 Copynumber: 3.0 Consensus size: 63
29812695 GGGTTTATAA
* ** *
29812705 TTTTTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTT
1 TTTTTTGTCT-AATTAGGCCTTAGGCTTGACAATTATTCTAACATTACGGCTTATACTTTTTTT
* * * * ** * * * *
29812769 GTTGTTGTCTAAGTTAGACTTTA-AATGTGACAATTGTTGTCACATTACGGTTTATACTCTTTTT
1 TTTTTTGTCTAA-TTAGGCCTTAGGCT-TGACAATTATTCTAACATTACGGCTTATACT-TTTTT
29812833 T
63 T
* * *
29812834 TTTTTTTTCTATATTAGGCCTTAGGCTTGACAATTATTCTAACATT-GGAGCTTGTACTTTTTTT
1 TTTTTTGTCTA-ATTAGGCCTTAGGCTTGACAATTATTCTAACATTACG-GCTTATACTTTTTTT
29812898 GTCAAAGTTA
Statistics
Matches: 96, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
63 3 0.03
64 46 0.48
65 45 0.47
66 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (63 bp):
TTTTTTGTCTAATTAGGCCTTAGGCTTGACAATTATTCTAACATTACGGCTTATACTTTTTTT
Found at i:29837735 original size:60 final size:59
Alignment explanation
Indices: 29837609--29837740 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 59
29837599 AGATCTTACT
** * * * *
29837609 AGCCTCCACCATAGGTTTTCACTCAATACAATTCTCCAAGCTAGCTTCCCAATCTTTTCC
1 AGCCTCCA-CATAGACTTCCACTCAATACAATTCTCCAAGCTAGCTTCCCAACCTTGTCA
* *
29837669 AGCCTCCAGCATAGACTTCCACTCAATATAATTCTCCAAGCTATCTTCCCAACCTTAGT-A
1 AGCCTCCA-CATAGACTTCCACTCAATACAATTCTCCAAGCTAGCTTCCCAACCTT-GTCA
*
29837729 ATCCTCCACATA
1 AGCCTCCACATA
29837741 CATATTTCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 4 0.07
60 56 0.92
61 1 0.02
ACGTcount: A:0.28, C:0.35, G:0.08, T:0.30
Consensus pattern (59 bp):
AGCCTCCACATAGACTTCCACTCAATACAATTCTCCAAGCTAGCTTCCCAACCTTGTCA
Found at i:29843648 original size:17 final size:16
Alignment explanation
Indices: 29843626--29843659 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29843616 ATTATATAAT
29843626 TAATGATAATTAAATTA
1 TAATGAT-ATTAAATTA
*
29843643 TAATGATATTATATTA
1 TAATGATATTAAATTA
29843659 T
1 T
29843660 TAAATAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATATTAAATTA
Found at i:29844545 original size:92 final size:92
Alignment explanation
Indices: 29844386--29844567 Score: 337
Period size: 92 Copynumber: 2.0 Consensus size: 92
29844376 CCAACAAAAA
*
29844386 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTATAA
1 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTACAA
*
29844451 GGAGAAGCGTATCTCTGGTGGGAATAT
66 GGAGAAACGTATCTCTGGTGGGAATAT
*
29844478 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTATTACAA
1 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTACAA
29844543 GGAGAAACGTATCTCTGGTGGGAAT
66 GGAGAAACGTATCTCTGGTGGGAAT
29844568 CTGTGGTTAG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (92 bp):
GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTACAA
GGAGAAACGTATCTCTGGTGGGAATAT
Found at i:29849127 original size:16 final size:17
Alignment explanation
Indices: 29849096--29849133 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
29849086 TTTAATATAT
29849096 AATTA-AATGATAATTA
1 AATTATAATGATAATTA
29849112 AATTATAATGAT-ATTA
1 AATTATAATGATAATTA
*
29849128 TATTAT
1 AATTAT
29849134 TAAATAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
AATTATAATGATAATTA
Found at i:29851875 original size:7 final size:7
Alignment explanation
Indices: 29851856--29851888 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
29851846 TTAAAATAAA
29851856 TAAATTT
1 TAAATTT
29851863 TAAAATTT
1 T-AAATTT
29851871 TAAATTT
1 TAAATTT
29851878 TAAATTT
1 TAAATTT
29851885 TAAA
1 TAAA
29851889 CATTAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:29857605 original size:12 final size:12
Alignment explanation
Indices: 29857588--29857617 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29857578 TAGGTAGTAA
29857588 AAGAAAAAGAAG
1 AAGAAAAAGAAG
29857600 AAGAAAAAGAAG
1 AAGAAAAAGAAG
29857612 -AGAAAA
1 AAGAAAA
29857618 TCTTTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAG
Found at i:29862566 original size:31 final size:29
Alignment explanation
Indices: 29862528--29862603 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
29862518 TTAATGGCTC
* *
29862528 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
29862559 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
29862588 AGTGACTAAAATGTAA
1 AGTGACTAAAATGTAA
29862604 TTTGAGCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.54
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:29872581 original size:19 final size:19
Alignment explanation
Indices: 29872539--29872596 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
29872529 TCTCTCTAAG
*
29872539 AAAAATACAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
29872558 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
29872577 AAAAAATTCCAAA-ATTTAT
1 -AAAAATTCAAAATATTTAT
29872596 A
1 A
29872597 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 5 0.15
19 18 0.55
20 10 0.30
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:29872584 original size:20 final size:19
Alignment explanation
Indices: 29872559--29872596 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
29872549 AATAATTTTT
29872559 AAAATTCAAAATATTTATAA
1 AAAATTCAAAA-ATTTATAA
*
29872579 AAAATTCCAAAATTTATA
1 AAAATTCAAAAATTTATA
29872597 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAAATTTATAA
Found at i:29872610 original size:18 final size:19
Alignment explanation
Indices: 29872587--29872634 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
29872577 AAAAAATTCC
*
29872587 AAAATT-TATATTTTTAAA
1 AAAATTATAAATTTTTAAA
29872605 AAAATTATAAATTTTTAAA
1 AAAATTATAAATTTTTAAA
*
29872624 AAAATTCTAAA
1 AAAATTATAAA
29872635 GAATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTATAAATTTTTAAA
Found at i:29883033 original size:3 final size:3
Alignment explanation
Indices: 29883025--29883057 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29883015 TGCACGGTTT
29883025 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
29883058 TTTACTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:29884150 original size:24 final size:24
Alignment explanation
Indices: 29884122--29884167 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29884112 AAATATTATT
29884122 TTATTTTATTGAATACTAATATGA
1 TTATTTTATTGAATACTAATATGA
* *
29884146 TTATTTTATTTAATATTAATAT
1 TTATTTTATTGAATACTAATAT
29884168 TAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTTTATTGAATACTAATATGA
Found at i:29884269 original size:53 final size:51
Alignment explanation
Indices: 29884197--29884326 Score: 131
Period size: 53 Copynumber: 2.5 Consensus size: 51
29884187 ATTATTATCT
* * *
29884197 TTTTTATATATTTTAAAATTTTGTA-TATTATTTTTGT-AAACAGTGTTT-TTTA
1 TTTTTATATATTTTTAAATTTT-TATTA-TATTTTTGTGAAA-A-TATTTATGTA
*
29884249 TTTTTATATACTTTTTAAATTTATTATTATATTTTTTTGAAAATATTTATGTA
1 TTTTTATATA-TTTTTAAATTT-TTATTATATTTTTGTGAAAATATTTATGTA
29884302 TTTTTATATATTTCTTTAAATTTTT
1 TTTTTATATA-TT-TTTAAATTTTT
29884327 TAAATTAGGA
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
52 14 0.21
53 38 0.57
54 15 0.22
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (51 bp):
TTTTTATATATTTTTAAATTTTTATTATATTTTTGTGAAAATATTTATGTA
Found at i:29894097 original size:16 final size:16
Alignment explanation
Indices: 29894078--29894109 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29894068 TTTTAAATTA
29894078 TAATTGTTTTTTATTT
1 TAATTGTTTTTTATTT
*
29894094 TAATTTTTTTTTATTT
1 TAATTGTTTTTTATTT
29894110 GTCCAACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
TAATTGTTTTTTATTT
Found at i:29894305 original size:3 final size:3
Alignment explanation
Indices: 29894297--29894327 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29894287 TTTGTTACAA
29894297 AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29894328 AACATCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29894317 original size:17 final size:17
Alignment explanation
Indices: 29894295--29894327 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29894285 AGTTTGTTAC
29894295 AAAATAATAATAATAAT
1 AAAATAATAATAATAAT
29894312 AAAATAATAATAATAA
1 AAAATAATAATAATAA
29894328 AACATCAAGT
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAATAATAATAAT
Found at i:29894319 original size:14 final size:14
Alignment explanation
Indices: 29894300--29894329 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29894290 GTTACAAAAT
29894300 AATAATAATAATAA
1 AATAATAATAATAA
29894314 AATAATAATAATAA
1 AATAATAATAATAA
29894328 AA
1 AA
29894330 CATCAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:29894389 original size:68 final size:69
Alignment explanation
Indices: 29894308--29894528 Score: 288
Period size: 68 Copynumber: 3.1 Consensus size: 69
29894298 ATAATAATAA
* *
29894308 TAATAAAATAATAATAATAAAACATCAAGTTTGTTCTACTAATCAAATGTTAGATTTTGTTACAA
1 TAATACAATAATAATAATAAAACATCAAGTTTGTTTTACTAATCAAATGTTAGATTTTGTTACAA
29894373 CAAT
66 CAAT
* *
29894377 TAATACAA-AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTATATTTTGTTACAA
1 TAATACAATAATAATAATAAAACATCAAGTTTGTTTTACTAATCAAATGTTAGATTTTGTTACAA
29894441 CAAT
66 CAAT
*
29894445 TAATACAATTAACAACTAATACAATTA-AT-AA-TTTGATAATTTTACTAATCAAATGTTAGATT
1 TAATACAA-TAATAA-TAATA-AA--ACATCAAGTTTG----TTTTACTAATCAAATGTTAGATT
29894507 TTGTTACAACAAT
57 TTGTTACAACAAT
29894520 TAATACAAT
1 TAATACAAT
29894529 TAACAAGTAA
Statistics
Matches: 135, Mismatches: 7, Indels: 15
0.86 0.04 0.10
Matches are distributed among these distances:
68 65 0.48
69 7 0.05
70 4 0.03
71 8 0.06
72 4 0.03
73 2 0.01
74 2 0.01
75 43 0.32
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (69 bp):
TAATACAATAATAATAATAAAACATCAAGTTTGTTTTACTAATCAAATGTTAGATTTTGTTACAA
CAAT
Found at i:29894464 original size:16 final size:16
Alignment explanation
Indices: 29894439--29894472 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29894429 ATTTTGTTAC
*
29894439 AACAATTAATACAATT
1 AACAACTAATACAATT
29894455 AACAACTAATACAATT
1 AACAACTAATACAATT
29894471 AA
1 AA
29894473 TAATTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AACAACTAATACAATT
Found at i:29894568 original size:16 final size:16
Alignment explanation
Indices: 29894547--29894588 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
29894537 AATAATTTGA
*
29894547 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
29894563 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
29894579 TAGTTTTAAT
1 TAATTTTAAT
29894589 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:29895533 original size:19 final size:19
Alignment explanation
Indices: 29895506--29895545 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29895496 ATTTTAAAAA
29895506 AATTCTTTAT-ATATTCTTT
1 AATTCTTTATAATATT-TTT
*
29895525 AATTTTTTATAATATTTTT
1 AATTCTTTATAATATTTTT
29895544 AA
1 AA
29895546 AAATATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTCTTTATAATATTTTT
Found at i:29895572 original size:26 final size:26
Alignment explanation
Indices: 29895529--29895585 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
29895519 TTCTTTAATT
*
29895529 TTTTATAATATTTTTAAAAATATAAA
1 TTTTAGAATATTTTTAAAAATATAAA
* *
29895555 TTTTAGAAT-TTTTATAAAAATTTGAA
1 TTTTAGAATATTTT-TAAAAATATAAA
29895581 TTTTA
1 TTTTA
29895586 AAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTAGAATATTTTTAAAAATATAAA
Found at i:29897679 original size:22 final size:22
Alignment explanation
Indices: 29897654--29897697 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29897644 TAATTTCACT
*
29897654 GCTACAGTATCCAATCTCACCG
1 GCTACAGTAACCAATCTCACCG
*
29897676 GCTACAGTAACTAATCTCACCG
1 GCTACAGTAACCAATCTCACCG
29897698 CCACCGCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.23
Consensus pattern (22 bp):
GCTACAGTAACCAATCTCACCG
Found at i:29913221 original size:22 final size:22
Alignment explanation
Indices: 29913190--29913239 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
29913180 AATTTAAAAT
*
29913190 TTAATTATAAAAGTATATAATTA
1 TTAA-TATAAAAATATATAATTA
*
29913213 TTAATATAAAAATATATATTTA
1 TTAATATAAAAATATATAATTA
*
29913235 ATAAT
1 TTAAT
29913240 TTGTTGATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTAATATAAAAATATATAATTA
Found at i:29913825 original size:23 final size:22
Alignment explanation
Indices: 29913781--29913841 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
29913771 ATAATGATAT
* *
29913781 TATAATATATATTTTTGTATTAA
1 TATAA-ATATAATTTTATATTAA
29913804 TATAAATATAATTTTATAATTAA
1 TATAAATATAATTTTAT-ATTAA
* *
29913827 AATTAAATAAAATTT
1 TA-TAAATATAATTT
29913842 AAAAAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 10 0.31
23 11 0.34
24 11 0.34
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TATAAATATAATTTTATATTAA
Found at i:29914403 original size:21 final size:22
Alignment explanation
Indices: 29914364--29914404 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29914354 ATACATTTGT
* *
29914364 AATACTTATATTTATTTATTAA
1 AATACTTATATTAAATTATTAA
29914386 AATA-TTATATTAAATTATT
1 AATACTTATATTAAATTATT
29914405 GTTGTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AATACTTATATTAAATTATTAA
Found at i:29925568 original size:2 final size:2
Alignment explanation
Indices: 29925561--29925590 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29925551 ATGTGTACAT
29925561 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29925591 TGAAAGTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29935139 original size:16 final size:17
Alignment explanation
Indices: 29935102--29935139 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29935092 TAAATAAATC
*
29935102 ATTAAAAAGATAAAATA
1 ATTAAAAAGATAAAAAA
*
29935119 TTTAAAAA-ATAAAAAA
1 ATTAAAAAGATAAAAAA
29935135 ATTAA
1 ATTAA
29935140 TTCAATCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATTAAAAAGATAAAAAA
Found at i:29940458 original size:1 final size:1
Alignment explanation
Indices: 29940452--29940480 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
29940442 AAATAAAACC
29940452 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29940481 TCATATTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29940461 original size:17 final size:16
Alignment explanation
Indices: 29940430--29940479 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 16
29940420 TCGATCCATC
* *
29940430 AAACCAAAAGTAAAATA
1 AAACCAAAA-AAAAAAA
29940447 AAACCAAAAAAAAAAA
1 AAACCAAAAAAAAAAA
29940463 AAA--AAAAAAAAAAA
1 AAACCAAAAAAAAAAA
29940477 AAA
1 AAA
29940480 ATCATATTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 14 0.45
16 8 0.26
17 9 0.29
ACGTcount: A:0.86, C:0.08, G:0.02, T:0.04
Consensus pattern (16 bp):
AAACCAAAAAAAAAAA
Found at i:29940858 original size:13 final size:14
Alignment explanation
Indices: 29940840--29940872 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29940830 ATCAATTTAA
29940840 TTTTAAATA-AATT
1 TTTTAAATACAATT
*
29940853 TTTTAACTACAATT
1 TTTTAAATACAATT
29940867 TTTTAA
1 TTTTAA
29940873 TTACTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAATACAATT
Found at i:29954963 original size:67 final size:67
Alignment explanation
Indices: 29954832--29954963 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 67
29954822 GGTTATGGCA
* * * *
29954832 ACATAGAGGGTCCGCGAGGACATTAAGCATTTGGGTAAAATGTGTGAGACCATAGCTCGACTATG
1 ACATAGAGGGTCCACGAGGACATTAAACA-TTGGGTAAAATGTGTAAGACCATAGCTAGACTATG
29954897 ATG
65 ATG
* * * *
29954900 ACATAGAGGGTCCACTAGGACCTTAAACA-TGGTGTAAAATGTGTAAGACCATGGCTAGGCTATG
1 ACATAGAGGGTCCACGAGGACATTAAACATTGG-GTAAAATGTGTAAGACCATAGCTAGACTATG
29954964 GCAGCATATG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 3 0.05
67 27 0.49
68 25 0.45
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (67 bp):
ACATAGAGGGTCCACGAGGACATTAAACATTGGGTAAAATGTGTAAGACCATAGCTAGACTATGA
TG
Found at i:29956114 original size:3 final size:3
Alignment explanation
Indices: 29956106--29956168 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
29956096 ATCTTTATAT
29956106 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29956154 GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
29956169 AAGTTACATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29957553 original size:22 final size:22
Alignment explanation
Indices: 29957521--29957584 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
29957511 TAAAAAATAA
29957521 TTTTTCCCTATAAAAACTCAAG
1 TTTTTCCCTATAAAAACTCAAG
*
29957543 TTTTTCTCTATAAAAA-TCAAG
1 TTTTTCCCTATAAAAACTCAAG
** *
29957564 TAATTCCCTATAAAATCTCAA
1 TTTTTCCCTATAAAAACTCAA
29957585 ATTTATCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (22 bp):
TTTTTCCCTATAAAAACTCAAG
Found at i:29957562 original size:21 final size:21
Alignment explanation
Indices: 29957513--29957578 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
29957503 ATTAATTCTA
29957513 AAAAAT-AA-TTTTTCCCTAT
1 AAAAATCAAGTTTTTCCCTAT
*
29957532 AAAAACTCAAGTTTTTCTCTAT
1 AAAAA-TCAAGTTTTTCCCTAT
**
29957554 AAAAATCAAGTAATTCCCTAT
1 AAAAATCAAGTTTTTCCCTAT
29957575 AAAA
1 AAAA
29957579 TCTCAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.12
20 1 0.03
21 19 0.47
22 15 0.38
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAATCAAGTTTTTCCCTAT
Found at i:29962984 original size:20 final size:20
Alignment explanation
Indices: 29962950--29962991 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29962940 AACTATTTAA
** *
29962950 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
29962970 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
29962990 AT
1 AT
29962992 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:29965066 original size:15 final size:15
Alignment explanation
Indices: 29965046--29965074 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29965036 GAAGCGCTTG
29965046 ATAAATCTAAAGTTT
1 ATAAATCTAAAGTTT
29965061 ATAAATCTAAAGTT
1 ATAAATCTAAAGTT
29965075 GAACTTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
ATAAATCTAAAGTTT
Found at i:29968850 original size:370 final size:371
Alignment explanation
Indices: 29968168--29968911 Score: 1251
Period size: 370 Copynumber: 2.0 Consensus size: 371
29968158 GGAATGAGAT
*
29968168 TTCATTTGGAAAACACACCAACAAATTCTAATATTTTTTCTTTCCTTCCTTCATTTTCTAATATT
1 TTCATTTGGAAAACACACCAACAAATTCTAATATTCTTTCTTTCCTTCCTTCATTTTCTAATATT
29968233 ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
66 ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
* * *
29968298 TTACTCAGTGTATTGTGGACTATTCTCGTTAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
131 TTACTCAGTGCATAGTGGACTATTCTCGTCAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
* *
29968363 TCCTCGAGGTTAATTTGCTTGGAACTCATTTGCACATCGAAGATAGGTGGAGGCGAATATAACCT
196 TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGAGGCGAATATAACCT
*
29968428 TAAAGATAGTGACTTGATACACGCCTTGGAGTCTTGTCATATTTCTTCTTTTTCTGTTCGAGTTC
261 TAAAGATAGTGACTTGATACACGCCTTGGAGCCTTGTCATATTTCTTCTTTTTCTGTTCGAGTTC
29968493 CGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTTCG-ACTAACAA
326 CGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTT-GAACTAACAA
* * *
29968539 TTCATTTGGAAGACACACCAACAAATTCTTATATTCTTTCTTTCCTTCCTTCATTTTCTAATGTT
1 TTCATTTGGAAAACACACCAACAAATTCTAATATTCTTTCTTTCCTTCCTTCATTTTCTAATATT
* * *
29968604 ATTAGATTATTCTATAAAGTATTACTGTAGAAATCCTTTGTAGAAATTGAGTTTCTTGTTATACA
66 ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
* *
29968669 TTGCTCAGTGCATAGTGGACTATTC-CGTCAGTGCAAAACGCAAATAGTCATTGGCTTCATTGTA
131 TTACTCAGTGCATAGTGGACTATTCTCGTCAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
*
29968733 TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGGGGCGAATATAACCT
196 TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGAGGCGAATATAACCT
* *
29968798 TAAAGATAGT-AGCTTGATACACGCCTTGGAGCCTTGTCCTATTTCTTCTTTTTCTGTTTGAGTT
261 TAAAGATAGTGA-CTTGATACACGCCTTGGAGCCTTGTCATATTTCTTCTTTTTCTGTTCGAGTT
* * * *
29968862 CCGTTCGTGTGTTCGAGATTTTTCTTACCGGAGATTTGAACTAACAA
325 CCGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTTGAACTAACAA
29968909 TTC
1 TTC
29968912 CAACTATTAT
Statistics
Matches: 349, Mismatches: 22, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
369 2 0.01
370 202 0.58
371 145 0.42
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (371 bp):
TTCATTTGGAAAACACACCAACAAATTCTAATATTCTTTCTTTCCTTCCTTCATTTTCTAATATT
ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
TTACTCAGTGCATAGTGGACTATTCTCGTCAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGAGGCGAATATAACCT
TAAAGATAGTGACTTGATACACGCCTTGGAGCCTTGTCATATTTCTTCTTTTTCTGTTCGAGTTC
CGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTTGAACTAACAA
Found at i:29973679 original size:31 final size:29
Alignment explanation
Indices: 29973609--29973665 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
29973599 AAATTGAATT
*
29973609 AAATCAATATTTTATATATAAAATTACACA
1 AAATCAA-AATTTATATATAAAATTACACA
*
29973639 AAATTAAAATTTATATATAAAATTACA
1 AAATCAAAATTTATATATAAAATTACA
29973666 TTGAAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTACACA
Found at i:29973685 original size:31 final size:29
Alignment explanation
Indices: 29973621--29973685 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
29973611 ATCAATATTT
* *
29973621 TATATATAAAATTACACAAAATTAAAATT
1 TATATATAAAATTACACAAAATCAAAATC
* *
29973650 TATATATAAAATTACATTGAAAGTCAAAATC
1 TATATATAAAATTACA--CAAAATCAAAATC
29973681 TATAT
1 TATAT
29973686 CTAACTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
31 14 0.47
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
TATATATAAAATTACACAAAATCAAAATC
Found at i:29982485 original size:32 final size:30
Alignment explanation
Indices: 29982429--29982487 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
29982419 TAACAATTAG
*
29982429 AAATTAATTAAATACGAATGTTTTAATAAT
1 AAATTAATTAAATACGAATATTTTAATAAT
*
29982459 AAATGTAATATAAATATGAATATTTTAAT
1 AAAT-TAAT-TAAATACGAATATTTTAAT
29982488 TATCTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 4 0.16
32 17 0.68
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (30 bp):
AAATTAATTAAATACGAATATTTTAATAAT
Found at i:29985235 original size:25 final size:26
Alignment explanation
Indices: 29985147--29985228 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
29985137 TAAGAGCTAC
* * * * *
29985147 AATCAGGAAGTTCACAAAGAACTTTT
1 AATCAAGAAGCTCACGAAGAGCCTTT
29985173 AATCAAGAAGCTCA-GAAGAGCCTTT
1 AATCAAGAAGCTCACGAAGAGCCTTT
*
29985198 AAACAAGAAGCTCACGAAGAGCCTTT
1 AATCAAGAAGCTCACGAAGAGCCTTT
29985224 AATCA
1 AATCA
29985229 GGAGCTCCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 21 0.44
26 27 0.56
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.21
Consensus pattern (26 bp):
AATCAAGAAGCTCACGAAGAGCCTTT
Found at i:29985813 original size:11 final size:11
Alignment explanation
Indices: 29985799--29985824 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29985789 TTAACATCAA
29985799 TTCATGTTCAT
1 TTCATGTTCAT
29985810 TTCATGTTCAT
1 TTCATGTTCAT
29985821 TTCA
1 TTCA
29985825 ATTCAATTCA
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:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (11 bp):
TTCATGTTCAT
Found at i:29986960 original size:8 final size:8
Alignment explanation
Indices: 29986947--29986975 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29986937 TTTAAAATGA
29986947 TATTTTAT
1 TATTTTAT
29986955 TATTTTAT
1 TATTTTAT
29986963 TATTTTAT
1 TATTTTAT
29986971 TATTT
1 TATTT
29986976 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:29990477 original size:13 final size:13
Alignment explanation
Indices: 29990459--29990497 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
29990449 GAAAGGTTAT
29990459 TTTAAAAATCATG
1 TTTAAAAATCATG
29990472 TTTAAAAAT-A--
1 TTTAAAAATCATG
29990482 TTTAAAAATCATG
1 TTTAAAAATCATG
29990495 TTT
1 TTT
29990498 TCCTTCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
12 1 0.04
13 12 0.52
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (13 bp):
TTTAAAAATCATG
Found at i:29990559 original size:2 final size:2
Alignment explanation
Indices: 29990552--29990578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29990542 TGCTGATACA
29990552 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29990579 GTGTCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29991736 original size:31 final size:29
Alignment explanation
Indices: 29991666--29991722 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
29991656 AAATTGAATT
*
29991666 AAATCAATATTTTATATATAAAATTACACA
1 AAATCAA-AATTTATATATAAAATTACACA
*
29991696 AAATTAAAATTTATATATAAAATTACA
1 AAATCAAAATTTATATATAAAATTACA
29991723 TTGAAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTACACA
Found at i:29991742 original size:31 final size:29
Alignment explanation
Indices: 29991678--29991742 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
29991668 ATCAATATTT
* *
29991678 TATATATAAAATTACACAAAATTAAAATT
1 TATATATAAAATTACACAAAATCAAAATC
* *
29991707 TATATATAAAATTACATTGAAAGTCAAAATC
1 TATATATAAAATTACA--CAAAATCAAAATC
29991738 TATAT
1 TATAT
29991743 CTAACTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
31 14 0.47
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
TATATATAAAATTACACAAAATCAAAATC
Found at i:29998436 original size:15 final size:16
Alignment explanation
Indices: 29998416--29998445 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29998406 CAGAAAGCCA
29998416 ATATTA-AAATTTTAT
1 ATATTATAAATTTTAT
29998431 ATATTATAAATTTTA
1 ATATTATAAATTTTA
29998446 ATAAAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTATAAATTTTAT
Found at i:30003675 original size:25 final size:25
Alignment explanation
Indices: 30003646--30003693 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
30003636 GTTAATACTA
*
30003646 TTAAAAGTGTTTTGTTAAATTCAAG
1 TTAAAAGTATTTTGTTAAATTCAAG
30003671 TTAAAAGTATTTTGTTAAATTCA
1 TTAAAAGTATTTTGTTAAATTCA
30003694 GGTTGACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (25 bp):
TTAAAAGTATTTTGTTAAATTCAAG
Found at i:30004448 original size:20 final size:20
Alignment explanation
Indices: 30004423--30004461 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30004413 CCCTTTTAAT
* *
30004423 TTTCCATCATTCTATTTTTC
1 TTTCCACCATTCCATTTTTC
30004443 TTTCCACCATTCCATTTTT
1 TTTCCACCATTCCATTTTT
30004462 TGAACAGGTT
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:0.15, C:0.28, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTCCACCATTCCATTTTTC
Found at i:30005352 original size:7 final size:7
Alignment explanation
Indices: 30005340--30005366 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30005330 TGTAATGGGT
30005340 TTAGGGC
1 TTAGGGC
30005347 TTAGGGC
1 TTAGGGC
30005354 TTAGGGC
1 TTAGGGC
30005361 TTAGGG
1 TTAGGG
30005367 TTTCTGTTTA
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:0.11, G:0.44, T:0.30
Consensus pattern (7 bp):
TTAGGGC
Found at i:30005746 original size:43 final size:43
Alignment explanation
Indices: 30005698--30005869 Score: 317
Period size: 43 Copynumber: 4.0 Consensus size: 43
30005688 CAAAATAAAA
* * *
30005698 ATGAAAATGGAAAAATGGAATCATTTGGAAATGAATGTGGTTT
1 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
30005741 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
1 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
30005784 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
1 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
30005827 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
1 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
30005870 TCTCCAAAAA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 126 1.00
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.28
Consensus pattern (43 bp):
ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
Found at i:30027510 original size:16 final size:17
Alignment explanation
Indices: 30027489--30027524 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
30027479 CATTAATTTA
*
30027489 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
30027505 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
30027522 AAT
1 AAT
30027525 CCAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:30033934 original size:3 final size:3
Alignment explanation
Indices: 30033926--30034015 Score: 69
Period size: 3 Copynumber: 30.0 Consensus size: 3
30033916 ATATTGCATC
* *
30033926 ATT ATT ATT -GT ATT ATT ATTT ATT ATT ATT A-T AGT AGTT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A-TT ATT ATT
* * ** *
30033971 ATT ATT ACT ATT CTT ATT GCT ATT AATG A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
30034016 TATATATATT
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
2 4 0.06
3 57 0.84
4 7 0.10
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:30033952 original size:21 final size:20
Alignment explanation
Indices: 30033926--30034015 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 20
30033916 ATATTGCATC
30033926 ATTATTATTGTATTATTATTT
1 ATTATTATTGTATTATTA-TT
* *
30033947 ATTATTATTATAGTAGTTATT
1 ATTATTATTGTATTA-TTATT
* *
30033968 ATTATTATTACTATTCTTATT
1 ATTATTATT-GTATTATTATT
** *
30033989 GCTATTAATGATATTATTATT
1 ATTATTATTG-TATTATTATT
30034010 ATTATT
1 ATTATT
30034016 TATATATATT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
21 48 0.89
22 6 0.11
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (20 bp):
ATTATTATTGTATTATTATT
Found at i:30034020 original size:18 final size:19
Alignment explanation
Indices: 30033926--30034026 Score: 64
Period size: 21 Copynumber: 5.1 Consensus size: 19
30033916 ATATTGCATC
*
30033926 ATTATTATTGTATTATTATTT
1 ATTATTATT-TACTATTA-TT
*
30033947 ATTATTATTATAGTAGTTATT
1 ATTATTATT-TACTA-TTATT
*
30033968 ATTATTA-TTACTATTCTT
1 ATTATTATTTACTATTATT
* *
30033986 ATTGCTATTAATGA-TATTATT
1 A-T--TATTATTTACTATTATT
30034007 ATTATTATTTA-TATATATT
1 ATTATTATTTACTAT-TATT
30034026 A
1 A
30034027 ATTTACTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
18 15 0.23
19 10 0.15
20 2 0.03
21 34 0.52
22 5 0.08
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTATTATTTACTATTATT
Found at i:30040098 original size:19 final size:19
Alignment explanation
Indices: 30040071--30040109 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
30040061 GATTATAATA
*
30040071 TAATTTTTAAAATTTGAAT
1 TAATATTTAAAATTTGAAT
30040090 TAATATTTAAAATTTGAAT
1 TAATATTTAAAATTTGAAT
30040109 T
1 T
30040110 TCCTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATATTTAAAATTTGAAT
Found at i:30042912 original size:85 final size:85
Alignment explanation
Indices: 30042769--30042938 Score: 306
Period size: 85 Copynumber: 2.0 Consensus size: 85
30042759 GGGGTCATGA
* *
30042769 CTCTAAACTAAATGTATATGAATTTCTTTTAACTTGTAAATAAATTTATTTTGTTATAATTTTTT
1 CTCTAAACTAAATGTATATGAATTCCTTTTAACTTCTAAATAAATTTATTTTGTTATAA-TTTTT
30042834 AAAAATTATT-AAATATATTT
65 AAAAATTATTAAAATATATTT
30042854 CTCTAAACTAAATGTATATGAATTCCTTTTAACTTCTAAATAAATTTATTTTGTTATAATTTTTA
1 CTCTAAACTAAATGTATATGAATTCCTTTTAACTTCTAAATAAATTTATTTTGTTATAATTTTTA
30042919 AAAATTATTAAAATATATTT
66 AAAATTATTAAAATATATTT
30042939 TTATAATTAA
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
84 15 0.18
85 67 0.82
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (85 bp):
CTCTAAACTAAATGTATATGAATTCCTTTTAACTTCTAAATAAATTTATTTTGTTATAATTTTTA
AAAATTATTAAAATATATTT
Found at i:30044549 original size:16 final size:16
Alignment explanation
Indices: 30044528--30044561 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
30044518 ATACGAGAGA
30044528 TTACCAAAATTCTGCT
1 TTACCAAAATTCTGCT
30044544 TTACCAAAATTCTGCT
1 TTACCAAAATTCTGCT
30044560 TT
1 TT
30044562 GGTTGTGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (16 bp):
TTACCAAAATTCTGCT
Found at i:30049481 original size:15 final size:16
Alignment explanation
Indices: 30049451--30049483 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30049441 GGTTCCAGAA
*
30049451 CTCTCTTTTTTCATAT
1 CTCTCTTTTTTAATAT
30049467 CTCTC-TTTTTAATAT
1 CTCTCTTTTTTAATAT
30049482 CT
1 CT
30049484 TGATTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (16 bp):
CTCTCTTTTTTAATAT
Found at i:30069862 original size:76 final size:72
Alignment explanation
Indices: 30069601--30069859 Score: 285
Period size: 69 Copynumber: 3.5 Consensus size: 72
30069591 TTTTTGGTAA
* * * *
30069601 ATTGTAAATAAGTATATATCATTGATGTAAAGTACAATAAAATACAATATAAACAATTTTTCATA
1 ATTGTAAATAAGTATAT-T-ATTGATGTAAAATACAATAAAATACAATACAAACAATTTTTTATT
30069666 TTTTT-T--
64 TTTTTCTAG
* * *
30069672 ATTGTAAATAAGTATATTATTGA-G-AAGACATGCGATAAAATACAATACAAATAATTTTTTATT
1 ATTGTAAATAAGTATATTATTGATGTAA-A-ATACAATAAAATACAATACAAACAATTTTTTATT
30069735 TTTTTCTTAG
64 TTTTTC-TAG
* * * *
30069745 ATTGTAAATAAGTATATATTATTAATATAAAATACAATAGAATACAAAACAAACAATTTTTTTAA
1 ATTGTAAATAAG--TATATTATTGATGTAAAATACAATAAAATACAATACAAACAA-TTTTTT--
30069810 ATTTTTTTCATAG
61 ATTTTTTTC-TAG
30069823 ATTGTAAATAAGTATATTATTGATGTAAAATACAATA
1 ATTGTAAATAAGTATATTATTGATGTAAAATACAATA
30069860 GAAAATCTTT
Statistics
Matches: 158, Mismatches: 17, Indels: 21
0.81 0.09 0.11
Matches are distributed among these distances:
67 2 0.01
68 2 0.01
69 37 0.23
70 1 0.01
71 18 0.11
73 12 0.08
75 30 0.19
76 30 0.19
77 2 0.01
78 24 0.15
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (72 bp):
ATTGTAAATAAGTATATTATTGATGTAAAATACAATAAAATACAATACAAACAATTTTTTATTTT
TTTCTAG
Found at i:30073328 original size:9 final size:9
Alignment explanation
Indices: 30073314--30073398 Score: 109
Period size: 9 Copynumber: 9.4 Consensus size: 9
30073304 TTTGGTTAAA
*
30073314 AATTAACTG
1 AATTAACCG
30073323 AATTAACCG
1 AATTAACCG
*
30073332 AATTACCCG
1 AATTAACCG
*
30073341 AATTAACTG
1 AATTAACCG
30073350 AATTAACCG
1 AATTAACCG
* *
30073359 GATTACCCG
1 AATTAACCG
30073368 AATTAACCG
1 AATTAACCG
30073377 AATT-ACCTG
1 AATTAACC-G
30073386 AATTAACCG
1 AATTAACCG
30073395 AATT
1 AATT
30073399 GAATCACTAC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
8 3 0.05
9 59 0.91
10 3 0.05
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:30073352 original size:27 final size:27
Alignment explanation
Indices: 30073314--30073398 Score: 127
Period size: 27 Copynumber: 3.1 Consensus size: 27
30073304 TTTGGTTAAA
30073314 AATTAACTGAATTAACCGAATTACCCG
1 AATTAACTGAATTAACCGAATTACCCG
*
30073341 AATTAACTGAATTAACCGGATTACCCG
1 AATTAACTGAATTAACCGAATTACCCG
* *
30073368 AATTAACCGAATT-ACCTGAATTAACCG
1 AATTAACTGAATTAACC-GAATTACCCG
30073395 AATT
1 AATT
30073399 GAATCACTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
26 3 0.06
27 50 0.94
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (27 bp):
AATTAACTGAATTAACCGAATTACCCG
Found at i:30077611 original size:2 final size:2
Alignment explanation
Indices: 30077604--30077632 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30077594 CAACAAGAGG
30077604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30077633 CAAGAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30084399 original size:13 final size:13
Alignment explanation
Indices: 30084378--30084432 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
30084368 TTAAAGTTAG
*
30084378 ATTATTATATTAT
1 ATTAGTATATTAT
*
30084391 ATTAGTATATTTT
1 ATTAGTATATTAT
* *
30084404 ATTTATTATTTTA-
1 A-TTAGTATATTAT
30084417 ATTAG-ATATTAT
1 ATTAGTATATTAT
30084429 ATTA
1 ATTA
30084433 AGAAAGATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
11 5 0.15
12 7 0.21
13 13 0.39
14 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (13 bp):
ATTAGTATATTAT
Found at i:30085575 original size:13 final size:11
Alignment explanation
Indices: 30085541--30085579 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
30085531 TCAAACATTA
30085541 TTTCT-TCAAT
1 TTTCTCTCAAT
30085551 TTTCTCTCAAT
1 TTTCTCTCAAT
*
30085562 TTTCTCTCTAAA
1 TTTCTCTC-AAT
30085574 TTTCTC
1 TTTCTC
30085580 AAAGCTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 5 0.19
11 13 0.50
12 8 0.31
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTCTCTCAAT
Found at i:30087369 original size:18 final size:18
Alignment explanation
Indices: 30087346--30087388 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
30087336 TGTCAGGTGC
*
30087346 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
30087364 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
30087382 GTTTCCT
1 GTATCCT
30087389 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:30091032 original size:126 final size:125
Alignment explanation
Indices: 30090867--30091136 Score: 353
Period size: 126 Copynumber: 2.2 Consensus size: 125
30090857 GACCAAACAA
* *
30090867 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAACTTTTTTCAGTAATTTTGCTAACATTGCATC
1 GAACTACTGTAGAAAAAAAGCGTCCACGTGGGAACTTTTTTCAGTAATTTTGCTAACAGTGCATC
*
30090932 CTACTTGAAGCAATTTTGACACTATTTGTTCAGAATCATCTTCTCAAAAATATTTTTTCAG
66 CTACTTGAAGCAATTTTGACACTATTTGTTCAGAACCATCTTCTCAAAAATA-TTTTTCAG
* ** * *
30090993 GAACTACTGTAGAAAAAAAGTG-CCTACGTGGGAGTTTTTTTCAGTAATTTTGTTGACAGTGCAT
1 GAACTACTGTAGAAAAAAAGCGTCC-ACGTGGGAACTTTTTTCAGTAATTTTGCTAACAGTGCAT
* ** * * * * * *
30091057 CCTGCTTGAAGCGTTTTTTACATTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTCAT
65 CCTACTTGAAGCAATTTTGACACTATTTGTTCAGAACCATCTTCTCAAAAATATTTTTCAG
*
30091118 AAACTACTGTAGAAAAAAA
1 GAACTACTGTAGAAAAAAA
30091137 CAAAAGTTTT
Statistics
Matches: 125, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
125 27 0.22
126 98 0.78
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAAAGCGTCCACGTGGGAACTTTTTTCAGTAATTTTGCTAACAGTGCATC
CTACTTGAAGCAATTTTGACACTATTTGTTCAGAACCATCTTCTCAAAAATATTTTTCAG
Found at i:30091242 original size:34 final size:34
Alignment explanation
Indices: 30091204--30091295 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
30091194 TTAAAAAAAA
*
30091204 CTAAACCATAATTTAATTAATTT-TCTTAAAA-ACC
1 CTAAACC-TAATTTAATTTATTTAT-TTAAAATACC
*
30091238 CTAAACCTTAATTTAATTTATTTATTTAAAATTCC
1 CTAAACC-TAATTTAATTTATTTATTTAAAATACC
**
30091273 AAAAACCTAATTTAATTTATTTA
1 CTAAACCTAATTTAATTTATTTA
30091296 AAAAAAACCT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
34 43 0.84
35 8 0.16
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.43
Consensus pattern (34 bp):
CTAAACCTAATTTAATTTATTTATTTAAAATACC
Found at i:30091344 original size:15 final size:15
Alignment explanation
Indices: 30091324--30091354 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30091314 AACCTACCAA
30091324 AAACCAAAAAACCCT
1 AAACCAAAAAACCCT
30091339 AAACCAAAAAACCCT
1 AAACCAAAAAACCCT
30091354 A
1 A
30091355 GGGACTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.32, G:0.00, T:0.06
Consensus pattern (15 bp):
AAACCAAAAAACCCT
Found at i:30092578 original size:21 final size:21
Alignment explanation
Indices: 30092525--30092623 Score: 107
Period size: 21 Copynumber: 4.8 Consensus size: 21
30092515 TAGTGTTACG
*
30092525 ACATCAAAAGCCAATGTT-GC
1 ACATCAGAAGCCAATGTTGGC
*
30092545 ACA-CTAGAAGCCAATGTTGGT
1 ACATC-AGAAGCCAATGTTGGC
* *
30092566 ACATCATAAGCCAATG-TCGC
1 ACATCAGAAGCCAATGTTGGC
*
30092586 ACA-CTAGAAGCCAATGTTGGG
1 ACATC-AGAAGCCAATGTTGGC
30092607 ACATCAGAAGCCAATGT
1 ACATCAGAAGCCAATGT
30092624 CACAACATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.03
20 30 0.46
21 31 0.48
22 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
ACATCAGAAGCCAATGTTGGC
Found at i:30092582 original size:41 final size:41
Alignment explanation
Indices: 30092524--30092624 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
30092514 CTAGTGTTAC
*
30092524 GACATCAAAAGCCAATGTTGCACACTAGAAGCCAATGTTGG
1 GACATCAAAAGCCAATGTCGCACACTAGAAGCCAATGTTGG
* *
30092565 TACATCATAAGCCAATGTCGCACACTAGAAGCCAATGTTGG
1 GACATCAAAAGCCAATGTCGCACACTAGAAGCCAATGTTGG
*
30092606 GACATCAGAAGCCAATGTC
1 GACATCAAAAGCCAATGTC
30092625 ACAACATTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (41 bp):
GACATCAAAAGCCAATGTCGCACACTAGAAGCCAATGTTGG
Found at i:30096335 original size:23 final size:23
Alignment explanation
Indices: 30096282--30096354 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
30096272 GAAGTGCTAG
* ** *
30096282 AATGAATTGCACCGTAGTACCAG
1 AATGAATTGCACCGAAGTGTCAA
* *
30096305 AATAAATTGCACCAAAGTGTCAA
1 AATGAATTGCACCGAAGTGTCAA
**
30096328 AATGAATTGCATTGAAGTGTCAA
1 AATGAATTGCACCGAAGTGTCAA
30096351 AATG
1 AATG
30096355 CTCCCACCAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (23 bp):
AATGAATTGCACCGAAGTGTCAA
Found at i:30101313 original size:94 final size:94
Alignment explanation
Indices: 30101152--30101339 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
30101142 TAATCAAGTC
* * *
30101152 AATTTGACTTTTCATATGTTAAAGGAGTTTAGTGGTCCAAAAAGAAAAATAAATGAAGCATTATG
1 AATTTGACTTTTCACATGTAAAAGGAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTATG
30101217 GGCTTGACCAATTTGCATCCTTCAATGCT
66 GGCTTGACCAATTTGCATCCTTCAATGCT
30101246 AATTTGACTTTTCACATGTAAAAGGAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTATG
1 AATTTGACTTTTCACATGTAAAAGGAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTATG
*
30101311 GGCTTGACCAATTTGCATCCTTTAATGCT
66 GGCTTGACCAATTTGCATCCTTCAATGCT
30101340 TTCTCCACAC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (94 bp):
AATTTGACTTTTCACATGTAAAAGGAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTATG
GGCTTGACCAATTTGCATCCTTCAATGCT
Found at i:30105812 original size:6 final size:6
Alignment explanation
Indices: 30105801--30105829 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30105791 AACCCAACCC
30105801 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
30105830 CTTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:30106599 original size:15 final size:15
Alignment explanation
Indices: 30106579--30106612 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30106569 CTTTCATACC
30106579 TTTTTTTGTTCTT-TT
1 TTTTTTTGTT-TTGTT
30106594 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTT
30106609 TTTT
1 TTTT
30106613 ACTCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (15 bp):
TTTTTTTGTTTTGTT
Found at i:30106943 original size:21 final size:18
Alignment explanation
Indices: 30106896--30106946 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
30106886 ATTTTTTTAG
30106896 TTTT-TATTTTATTTTGT
1 TTTTCTATTTTATTTTGT
*
30106913 TTTTCCATTTTCATATTTGT
1 TTTTCTATTTT-AT-TTTGT
30106933 TTTCTCTATTTTAT
1 TTT-TCTATTTTAT
30106947 GTTTCTCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 5 0.18
19 2 0.07
20 10 0.36
21 7 0.25
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTCTATTTTATTTTGT
Found at i:30107812 original size:26 final size:28
Alignment explanation
Indices: 30107760--30107822 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
30107750 TTTAAAATAC
* * *
30107760 TTTTAAAATAATTTTTTTATTTTTTTAT
1 TTTTAAAATAATATTTTTATATGTTTAT
30107788 TTTTAAAATAA-ATTTTTA-ATGTTTAT
1 TTTTAAAATAATATTTTTATATGTTTAT
*
30107814 TTTAAAAAT
1 TTTTAAAAT
30107823 GGGCAGGCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 14 0.45
27 6 0.19
28 11 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTAAAATAATATTTTTATATGTTTAT
Found at i:30108018 original size:26 final size:28
Alignment explanation
Indices: 30107966--30108028 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
30107956 TTTAAAATAC
* * *
30107966 TTTTAAAATAATTTTTTTATTTTTTTAT
1 TTTTAAAATAATATTTTTATATGTTTAT
30107994 TTTTAAAATAA-ATTTTTA-ATGTTTAT
1 TTTTAAAATAATATTTTTATATGTTTAT
*
30108020 TTTAAAAAT
1 TTTTAAAAT
30108029 GGGCCGGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 14 0.45
27 6 0.19
28 11 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTAAAATAATATTTTTATATGTTTAT
Found at i:30110433 original size:19 final size:20
Alignment explanation
Indices: 30110390--30110450 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
30110380 ATGTCACATC
* *
30110390 AAAAAATAATTTAAAAACTA
1 AAAAAATAATTCAAAAAATA
*
30110410 TAAAAAT-ATTCAAAAAATAA
1 AAAAAATAATTCAAAAAAT-A
*
30110430 AAAAAATCAATTTAAAAAATA
1 AAAAAAT-AATTCAAAAAATA
30110451 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 9 0.27
20 13 0.39
21 1 0.03
22 10 0.30
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAATAATTCAAAAAATA
Found at i:30110448 original size:13 final size:11
Alignment explanation
Indices: 30110390--30110459 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
30110380 ATGTCACATC
30110390 AAAAAATAATTT
1 AAAAAAT-ATTT
*
30110402 AAAAACTA--T
1 AAAAAATATTT
*
30110411 -AAAAATATTC
1 AAAAAATATTT
*
30110421 AAAAAATA--A
1 AAAAAATATTT
30110430 AAAAAATCAATTT
1 AAAAAAT--ATTT
30110443 AAAAAATATTT
1 AAAAAATATTT
30110454 AAAAAA
1 AAAAAA
30110460 AAATGATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
8 6 0.13
9 8 0.17
11 19 0.41
12 6 0.13
13 7 0.15
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAAATATTT
Found at i:30125793 original size:25 final size:24
Alignment explanation
Indices: 30125765--30125824 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
30125755 TAAAGAACTA
* *
30125765 AATATATAAATTATTTTTATATGT
1 AATATATAAATTATTTGTATATAT
* * *
30125789 GAATAAATATAATTGTTTGTGTATAT
1 -AATATATA-AATTATTTGTATATAT
30125815 AATATATAAA
1 AATATATAAA
30125825 CATTAAATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 2 0.07
25 14 0.50
26 12 0.43
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (24 bp):
AATATATAAATTATTTGTATATAT
Found at i:30132784 original size:3 final size:3
Alignment explanation
Indices: 30132776--30132813 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
30132766 TCTATCTACT
30132776 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
30132814 TAATCTTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:30138603 original size:4 final size:4
Alignment explanation
Indices: 30138594--30138620 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
30138584 GGCAATTATA
30138594 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
30138621 ATACTGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:30139839 original size:11 final size:11
Alignment explanation
Indices: 30139823--30139847 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30139813 TAAAAACTTT
30139823 TTTTTAATATA
1 TTTTTAATATA
30139834 TTTTTAATATA
1 TTTTTAATATA
30139845 TTT
1 TTT
30139848 ATTTTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTAATATA
Found at i:30146306 original size:30 final size:27
Alignment explanation
Indices: 30146270--30146343 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 27
30146260 AACAGAAAGG
30146270 GACCAAAAAAAACATATCGATTAGTTGGGT
1 GACCAAAAAAAA-A-ATCGA-TAGTTGGGT
*
30146300 GACCAAATTAAAAAAATTGATAGTTGGGT
1 GACCAAA--AAAAAAATCGATAGTTGGGT
30146329 GACCAAAAAAGAAAA
1 GACCAAAAAA-AAAA
30146344 AAGACACTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 4 0.10
29 16 0.40
30 11 0.28
31 1 0.03
32 5 0.12
ACGTcount: A:0.50, C:0.11, G:0.19, T:0.20
Consensus pattern (27 bp):
GACCAAAAAAAAAATCGATAGTTGGGT
Found at i:30151026 original size:127 final size:128
Alignment explanation
Indices: 30150845--30151100 Score: 505
Period size: 127 Copynumber: 2.0 Consensus size: 128
30150835 TTTAAAAATA
30150845 AAAGTACACAAAGATATGAAAAGTTATATCTTTTAAGAGATAAATAATGCTATAAATAATGCTTT
1 AAAGTACACAAAGATATGAAAAGTTATATCTTTTAAGAGATAAATAATGCTATAAATAATGCTTT
30150910 AAACTATTTTAAGAATGCTTTAAGCTTTTTTTATTTCTATTATTTTAAATA-TTTAATTAATT
66 AAACTATTTTAAGAATGCTTTAAGCTTTTTTTATTTCTATTATTTTAAATATTTTAATTAATT
30150972 AAAGTACACAAAGATATGAAAAGTTATATCTTTTAAGAGATAAATAATGCTATAAATAATGCTTT
1 AAAGTACACAAAGATATGAAAAGTTATATCTTTTAAGAGATAAATAATGCTATAAATAATGCTTT
30151037 AAACTATTTTAAGAATGCTTTAAGCTTTTTTTATTTCTATTATTTTAAATATTTTAATTAATT
66 AAACTATTTTAAGAATGCTTTAAGCTTTTTTTATTTCTATTATTTTAAATATTTTAATTAATT
30151100 A
1 A
30151101 TATAAATATA
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 116 0.91
128 12 0.09
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (128 bp):
AAAGTACACAAAGATATGAAAAGTTATATCTTTTAAGAGATAAATAATGCTATAAATAATGCTTT
AAACTATTTTAAGAATGCTTTAAGCTTTTTTTATTTCTATTATTTTAAATATTTTAATTAATT
Found at i:30160695 original size:32 final size:34
Alignment explanation
Indices: 30160631--30160697 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
30160621 TTAGACATTT
* *
30160631 AGTATTTATATAATAAATATTTTTTTTATTTTAA
1 AGTATTTATAAAATAAATATTTTTTATATTTTAA
*
30160665 AGTATTTTTAAAATAAAT-TTTTTTAT-TTTTAA
1 AGTATTTATAAAATAAATATTTTTTATATTTTAA
30160697 A
1 A
30160698 ATACATTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 7 0.23
33 7 0.23
34 16 0.53
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (34 bp):
AGTATTTATAAAATAAATATTTTTTATATTTTAA
Found at i:30186345 original size:41 final size:41
Alignment explanation
Indices: 30186258--30186355 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 41
30186248 CTAACATTTA
* *
30186258 ATATATCAAGTTTTATACTTGAAAAGTATTTTTAATGTTCG
1 ATATGTCAAGTTTTATACTTGAAAAGTATTTTTAACGTTCG
* * * * *
30186299 ATATGTTAAGTTTTATAGTTGGAAAGTGTTTTTAACGTTTG
1 ATATGTCAAGTTTTATACTTGAAAAGTATTTTTAACGTTCG
* *
30186340 GTATGTCAAATTTTAT
1 ATATGTCAAGTTTTAT
30186356 TTACTTTTCC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (41 bp):
ATATGTCAAGTTTTATACTTGAAAAGTATTTTTAACGTTCG
Found at i:30187459 original size:20 final size:20
Alignment explanation
Indices: 30187436--30187503 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
30187426 AGTTTTTAAC
*
30187436 ACTTTTAATAGAATTT-TATA
1 ACTTTTAA-ACAATTTCTATA
30187456 ACTTTTTAAACAATTTCTATA
1 AC-TTTTAAACAATTTCTATA
* * * *
30187477 AATTTTATATATTTTTCTATA
1 ACTTTTAAACA-ATTTCTATA
30187498 ACTTTT
1 ACTTTT
30187504 CTTTATAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.54
Consensus pattern (20 bp):
ACTTTTAAACAATTTCTATA
Found at i:30187625 original size:10 final size:9
Alignment explanation
Indices: 30187606--30187670 Score: 67
Period size: 9 Copynumber: 7.0 Consensus size: 9
30187596 TGTTAATATC
30187606 TTATAATTT
1 TTATAATTT
30187615 TTATAATTT
1 TTATAATTT
30187624 TTATAATTT
1 TTATAATTT
*
30187633 TCTATTATTT
1 T-TATAATTT
* *
30187643 TCAAAATTT
1 TTATAATTT
*
30187652 TATATCATTT
1 T-TATAATTT
*
30187662 TAATAATTT
1 TTATAATTT
30187671 ATAGATTTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
9 31 0.69
10 14 0.31
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:30187629 original size:18 final size:19
Alignment explanation
Indices: 30187606--30187670 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
30187596 TGTTAATATC
30187606 TTATAATTTT-TATAATTT
1 TTATAATTTTATATAATTT
* *
30187624 TTATAATTTTCTATTATTT
1 TTATAATTTTATATAATTT
* * *
30187643 TCAAAATTTTATATCATTT
1 TTATAATTTTATATAATTT
*
30187662 TAATAATTT
1 TTATAATTT
30187671 ATAGATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 10 0.26
19 29 0.74
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATAATTTTATATAATTT
Found at i:30193318 original size:17 final size:17
Alignment explanation
Indices: 30193291--30193350 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
30193281 AAATGAAGAA
30193291 AAAAAGTAAGAAAGAAAT
1 AAAAAG-AAGAAAGAAAT
30193309 AAAAAGAAG-AA-AAAT
1 AAAAAGAAGAAAGAAAT
*
30193324 -TAAAGAA-AAAGAAATT
1 AAAAAGAAGAAAGAAA-T
30193340 AAAAA-AAGAAA
1 AAAAAGAAGAAA
30193351 TGATATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 8 0.23
15 7 0.20
16 5 0.14
17 9 0.26
18 6 0.17
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (17 bp):
AAAAAGAAGAAAGAAAT
Found at i:30193320 original size:13 final size:13
Alignment explanation
Indices: 30193301--30193351 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
30193291 AAAAAGTAAG
30193301 AAAGAAA-TAAAA
1 AAAGAAATTAAAA
30193313 AGAAGAAAAATTAAAGAA
1 A-AAG--AAATT-AA-AA
30193331 AAAGAAATTAAAA
1 AAAGAAATTAAAA
30193344 AAAGAAAT
1 AAAGAAAT
30193352 GATATTATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 1 0.03
13 13 0.39
14 2 0.06
15 8 0.24
16 1 0.03
17 5 0.15
18 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAGAAATTAAAA
Found at i:30195310 original size:10 final size:10
Alignment explanation
Indices: 30195295--30195320 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30195285 CTTACTGATC
30195295 TGTTAGTATT
1 TGTTAGTATT
30195305 TGTTAGTATT
1 TGTTAGTATT
30195315 TGTTAG
1 TGTTAG
30195321 CAGTTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTAGTATT
Found at i:30196908 original size:50 final size:50
Alignment explanation
Indices: 30196795--30197039 Score: 246
Period size: 50 Copynumber: 4.8 Consensus size: 50
30196785 ATTGGGGTAA
* *
30196795 AGAGATCCCATGTAATACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CG-TTATG
* * *
30196851 AGGGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGTTATG
* * * *
30196901 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGTTATG
* * * **
30196951 AGA-ACTCCCATGTAAGACCATATTTGGGATATGGCATTGGCA--G-TAAA
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGTTATG
* * *
30196998 AAAAATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30197040 TGTTATTATC
Statistics
Matches: 166, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
47 37 0.22
48 2 0.01
50 87 0.52
51 1 0.01
55 1 0.01
56 38 0.23
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGTTATG
Done.