Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 15
Found at i:878107 original size:16 final size:18
Alignment explanation
Indices: 878086--878120 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
878076 TTTACTCATT
878086 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
878102 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
878120 T
1 T
878121 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:881889 original size:21 final size:21
Alignment explanation
Indices: 881863--881903 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
881853 CACGATACTA
881863 ATATGACAATTTATAATATTG
1 ATATGACAATTTATAATATTG
*
881884 ATATGATAATTTATAATATT
1 ATATGACAATTTATAATATT
881904 AAGACGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (21 bp):
ATATGACAATTTATAATATTG
Found at i:884808 original size:23 final size:23
Alignment explanation
Indices: 884775--884837 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
884765 ATTATTATAT
884775 GGCACTACGGTGCAATTCTA-AGC
1 GGCACTACGGTGCAATTCTACA-C
* *
884798 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACAC
*
884821 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
884838 ATACGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:887235 original size:168 final size:168
Alignment explanation
Indices: 886983--887322 Score: 664
Period size: 168 Copynumber: 2.0 Consensus size: 168
886973 CTTATATTGC
886983 TTTT-GGATGTTGAGTGCCGCTTCGGGAGTGAGCTTATTGAGTGTAGAAGAATTGAAATATGCTC
1 TTTTGGGATGTTGAGTGCCGCTTCGGGAGTGAGCTTATTGAGTGTAGAAGAATTGAAATATGCTC
887047 AATTTATTTGAATTTGTAATAACCATGCAATTTGCTAACTTTTGTTTAATTTACAAGCTATTGAG
66 AATTTATTTGAATTTGTAATAACCATGCAATTTGCTAACTTTTGTTTAATTTACAAGCTATTGAG
*
887112 CTATACATTATTTATTTGGTTCCTTAATTATGTGCCAG
131 CTATACATTATTTATTTGGGTCCTTAATTATGTGCCAG
887150 TTTTGGGATGTTGAGTGCCGCTTCGGGAGTGAGCTTATTGAGTGTAGAAGAATTGAAATATGCTC
1 TTTTGGGATGTTGAGTGCCGCTTCGGGAGTGAGCTTATTGAGTGTAGAAGAATTGAAATATGCTC
887215 AATTTATTTGAATTTGTAATAACCATGCAATTTGCTAACTTTTGTTTAATTTACAAGCTATTGAG
66 AATTTATTTGAATTTGTAATAACCATGCAATTTGCTAACTTTTGTTTAATTTACAAGCTATTGAG
887280 CTATACATTATTTATTTGGGTCCTTAATTATGTGCCAG
131 CTATACATTATTTATTTGGGTCCTTAATTATGTGCCAG
887318 TTTTG
1 TTTTG
887323 AGGGCTATAT
Statistics
Matches: 171, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
167 4 0.02
168 167 0.98
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.41
Consensus pattern (168 bp):
TTTTGGGATGTTGAGTGCCGCTTCGGGAGTGAGCTTATTGAGTGTAGAAGAATTGAAATATGCTC
AATTTATTTGAATTTGTAATAACCATGCAATTTGCTAACTTTTGTTTAATTTACAAGCTATTGAG
CTATACATTATTTATTTGGGTCCTTAATTATGTGCCAG
Found at i:891848 original size:22 final size:22
Alignment explanation
Indices: 891822--891869 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
891812 ATAAATAAAT
891822 AAATAATAAACCTACCATTTTA
1 AAATAATAAACCTACCATTTTA
891844 AAATAATAAACCTACCATTTTA
1 AAATAATAAACCTACCATTTTA
891866 AAAT
1 AAAT
891870 TATTGTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAATAAACCTACCATTTTA
Found at i:893539 original size:20 final size:21
Alignment explanation
Indices: 893502--893541 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
893492 AAATTAAGTT
893502 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
893523 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
893542 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:893793 original size:19 final size:19
Alignment explanation
Indices: 893769--893807 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
893759 ACATCGAATG
893769 CATTCCATGCACCGATGCA
1 CATTCCATGCACCGATGCA
*
893788 CATTCCATGCATCGATGCA
1 CATTCCATGCACCGATGCA
893807 C
1 C
893808 TCTGAATATT
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:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (19 bp):
CATTCCATGCACCGATGCA
Found at i:893827 original size:65 final size:64
Alignment explanation
Indices: 893709--893918 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
893699 TATTCAAAGG
* * *
893709 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCA-CAATCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGCA
*
893771 TTC
62 TTT
*
893774 CATGCACCGATGCACATTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACAATCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * * * **
893839 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACAATCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
893903 CATGCATCGATGCACA
1 CATGCACCGATGCACA
893919 CTTGGTGCAC
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
63 7 0.05
64 55 0.43
65 66 0.52
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACAATCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:901336 original size:21 final size:21
Alignment explanation
Indices: 901294--901337 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
901284 ACCCCGGGAG
*
901294 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
901315 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
901336 CT
1 CT
901338 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:902072 original size:20 final size:21
Alignment explanation
Indices: 902035--902074 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
902025 AAATTAAGTT
902035 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
902056 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
902075 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:902318 original size:19 final size:19
Alignment explanation
Indices: 902294--902332 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
902284 ACATCGAATG
902294 CATTCCATGCACCGATGCA
1 CATTCCATGCACCGATGCA
*
902313 CATTCCATGCATCGATGCA
1 CATTCCATGCACCGATGCA
902332 C
1 C
902333 TCTGAATATT
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:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (19 bp):
CATTCCATGCACCGATGCA
Found at i:902438 original size:64 final size:65
Alignment explanation
Indices: 902283--902443 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
902273 GAATTAATTG
* * ** *
902283 AACATCGAATGCATTCCATGCACCGATGCACATTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
902348 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
902411 A
65 A
902412 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
902444 CTTGGTGCAC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 36 0.42
65 50 0.58
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:917609 original size:2 final size:2
Alignment explanation
Indices: 917602--917634 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
917592 AAGAAAAGAG
917602 TA TA TA TA 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 TA TA TA TA T
917635 TTACCTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:918581 original size:31 final size:30
Alignment explanation
Indices: 918541--918598 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
918531 TTTAAATTCT
918541 TATAAAATTTAATTATCTTTT-ATTTTTATTA
1 TATAAAATTTAA-TA-CTTTTAATTTTTATTA
* *
918572 TATATAATTTTATACTTTTAATTTTTA
1 TATAAAATTTAATACTTTTAATTTTTA
918599 AAAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 9 0.38
31 10 0.42
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TATAAAATTTAATACTTTTAATTTTTATTA
Found at i:918601 original size:54 final size:53
Alignment explanation
Indices: 918543--918646 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 53
918533 TAAATTCTTA
*
918543 TAAAATTTAATT-ATCTTTTATTT-TTATTATATATA-ATTTTATACTTTTAATTTT
1 TAAAAATTAATTAATCTTTTATTTGTT-TT-TA-ATACATTTTATA-TTTTAATTTT
*
918597 TAAAAATTAATTAAATTTTTTATTTGTTTTTAATACATTTTATATTTTAA
1 TAAAAATTAATT-AATCTTTTATTTGTTTTTAATACATTTTATATTTTAA
918647 GGTTAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
54 20 0.45
55 10 0.23
56 12 0.27
57 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (53 bp):
TAAAAATTAATTAATCTTTTATTTGTTTTTAATACATTTTATATTTTAATTTT
Found at i:919230 original size:2 final size:2
Alignment explanation
Indices: 919223--919248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
919213 TTTCAAAATA
919223 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
919249 TACAAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:922117 original size:25 final size:28
Alignment explanation
Indices: 922082--922145 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 28
922072 TTTACTTTTC
922082 AAATTATTTACTA-ATA-AAATATTTAT
1 AAATTATTTACTATATATAAATATTTAT
922108 -AATTATTTACTATCTATATAAATATTTAT
1 AAATTATTTACTA--TATATAAATATTTAT
922137 AAATTATTT
1 AAATTATTT
922146 TAACACATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 12 0.36
28 3 0.09
29 10 0.30
30 8 0.24
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (28 bp):
AAATTATTTACTATATATAAATATTTAT
Found at i:923230 original size:11 final size:12
Alignment explanation
Indices: 923200--923232 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
923190 AAATTATAAC
*
923200 ATATCAATATTT
1 ATATAAATATTT
923212 ATATAAATATTT
1 ATATAAATATTT
923224 A-ATAAATAT
1 ATATAAATAT
923233 AATACTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATAAATATTT
Found at i:924368 original size:71 final size:70
Alignment explanation
Indices: 924287--924426 Score: 201
Period size: 70 Copynumber: 2.0 Consensus size: 70
924277 CTTCTAAATT
* * * *
924287 TTTCAGGTTTTCCTATATTTTAGA-TTTTTGATGTATTCTTTTATTGATAATCTATTCTCGTCCT
1 TTTCAAGTTTTCCTATATTTTAGATTTTTTAATGTA-T-TTTTATTGATAATCTATTATCGCCCT
924351 TTAAAAA
64 TTAAAAA
* *
924358 TTTCAAGTTTTTCTATATTTTAGATTTTTTAATGTATTTTTATTGATAATTTATTATCGCCCTTT
1 TTTCAAGTTTTCCTATATTTTAGATTTTTTAATGTATTTTTATTGATAATCTATTATCGCCCTTT
924423 AAAA
66 AAAA
924427 TTTTATAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
70 29 0.47
71 23 0.37
72 10 0.16
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (70 bp):
TTTCAAGTTTTCCTATATTTTAGATTTTTTAATGTATTTTTATTGATAATCTATTATCGCCCTTT
AAAAA
Found at i:924716 original size:24 final size:23
Alignment explanation
Indices: 924689--924738 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
924679 TCAGTATGGT
*
924689 TTATC-TATATTCAATTTTAAATAA
1 TTATCATAAATTCAA-TTT-AATAA
*
924713 TTATCATAAATTTAATTTAATAA
1 TTATCATAAATTCAATTTAATAA
924736 TTA
1 TTA
924739 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 8 0.35
25 7 0.30
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATCATAAATTCAATTTAATAA
Found at i:925595 original size:13 final size:13
Alignment explanation
Indices: 925561--925597 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
925551 AAAATTTGTT
*
925561 ATAGTCATTATAA
1 ATAGTCATTGTAA
925574 ATA-TCATTGTAA
1 ATAGTCATTGTAA
925586 ATAGTCATTGTA
1 ATAGTCATTGTA
925598 GATAACAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (13 bp):
ATAGTCATTGTAA
Found at i:925828 original size:16 final size:16
Alignment explanation
Indices: 925807--925840 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
925797 TAAAGAGTTT
925807 AATCGTCAGATTCTGG
1 AATCGTCAGATTCTGG
925823 AATCGTCAGATTCTGG
1 AATCGTCAGATTCTGG
925839 AA
1 AA
925841 ATGGAGTTAG
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:0.18, G:0.24, T:0.29
Consensus pattern (16 bp):
AATCGTCAGATTCTGG
Found at i:927108 original size:20 final size:21
Alignment explanation
Indices: 927070--927109 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
927060 TATAATACAA
*
927070 AAAAAATCTATGATGTTTAACT
1 AAAAAATCTATCA-GTTTAACT
927092 AAAAAATCTATCA-TTTAA
1 AAAAAATCTATCAGTTTAA
927110 AGTGACACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAAATCTATCAGTTTAACT
Found at i:927916 original size:15 final size:16
Alignment explanation
Indices: 927896--927925 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
927886 TGTTAGTTAT
927896 TTGTTG-AAAACAAAA
1 TTGTTGCAAAACAAAA
927911 TTGTTGCAAAACAAA
1 TTGTTGCAAAACAAA
927926 TTATTTGTAT
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:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (16 bp):
TTGTTGCAAAACAAAA
Found at i:928974 original size:60 final size:61
Alignment explanation
Indices: 928879--929001 Score: 194
Period size: 60 Copynumber: 2.0 Consensus size: 61
928869 TAAAACTACA
*
928879 CATCAATTAAAATATTCACATTTGCATAAGCCGATGACCAACTCGATTAAACAATGACCTTT
1 CATCAATTAAAAGA-TCACATTTGCATAAGCCGATGACCAACTCGATTAAACAATGACCTTT
* * *
928941 CATCAATTAAAAGA-CACATTTGTATAAGCCGATGACCAATTCGCTTAAACAATGACCTTT
1 CATCAATTAAAAGATCACATTTGCATAAGCCGATGACCAACTCGATTAAACAATGACCTTT
929001 C
1 C
929002 TTCCCCAACT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 44 0.77
62 13 0.23
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (61 bp):
CATCAATTAAAAGATCACATTTGCATAAGCCGATGACCAACTCGATTAAACAATGACCTTT
Found at i:930297 original size:13 final size:13
Alignment explanation
Indices: 930279--930309 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
930269 CAATAATTGA
930279 TGTTACATACCTC
1 TGTTACATACCTC
930292 TGTTACATACCTC
1 TGTTACATACCTC
930305 TGTTA
1 TGTTA
930310 TGGCTAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.42
Consensus pattern (13 bp):
TGTTACATACCTC
Found at i:933030 original size:2 final size:2
Alignment explanation
Indices: 933023--933067 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
933013 AAGGAAAATA
933023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
933065 AT A
1 AT A
933068 GAGAGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:933072 original size:2 final size:2
Alignment explanation
Indices: 933067--933092 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
933057 ATATATATAT
933067 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
933093 GATTAGTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:934725 original size:171 final size:173
Alignment explanation
Indices: 934419--934738 Score: 518
Period size: 171 Copynumber: 1.8 Consensus size: 173
934409 CGGACGAAAG
934419 CTTAGGAACAAAACCAAAACAGTCGAAAACAATATCGATGTAGACGGTTCTTCACCACCATACAC
1 CTTAGGAACAAAACCAAAACAGTCGAAAACAATATCGATGTAGACGGTTCTTCACCACCATACAC
934484 TCTTTAAGTCCTTATGTAGCAGTCTATATGAGGGTAGAAATAGATTGGATGATTCATTGCAAGAA
66 -C--T---TCCTTATGTAGCAGTCTATATGAGGGTAGAAATAGATTGGATGATTCATTGCAAGAA
934549 CTTAGAGAAAAGATCAGCCGAAAACAAGGCAAGAACTTAGAGCAAAGAA
125 CTTAGAGAAAAGATCAGCCGAAAACAAGGCAAGAACTTAGAGCAAAGAA
* * * *
934598 CTTAGGAACAAAACCAAGACAGTCGAAAACAATTTCGATGTAGAGGGTTCTTCACCGCCATACA-
1 CTTAGGAACAAAACCAAAACAGTCGAAAACAATATCGATGTAGACGGTTCTTCACCACCATACAC
934662 C-TCCTTATGTAGCAGTCTATATGAGGGTAGAAATAGATTGGATGATTCATTGCAAGAACTTAGA
66 CTTCCTTATGTAGCAGTCTATATGAGGGTAGAAATAGATTGGATGATTCATTGCAAGAACTTAGA
* *
934726 GCAAATATCAGCC
131 GAAAAGATCAGCC
934739 CGATAAACCA
Statistics
Matches: 135, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
171 74 0.55
177 1 0.01
179 60 0.44
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (173 bp):
CTTAGGAACAAAACCAAAACAGTCGAAAACAATATCGATGTAGACGGTTCTTCACCACCATACAC
CTTCCTTATGTAGCAGTCTATATGAGGGTAGAAATAGATTGGATGATTCATTGCAAGAACTTAGA
GAAAAGATCAGCCGAAAACAAGGCAAGAACTTAGAGCAAAGAA
Found at i:945654 original size:2 final size:2
Alignment explanation
Indices: 945635--945672 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
945625 TGGTATGAAA
* *
945635 AT AT AA AT AT AT AA AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
945673 ATTGATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:947512 original size:42 final size:43
Alignment explanation
Indices: 947437--947528 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
947427 TATAGAATTG
* *
947437 AAAAAATTAGGTACTCAATTATAAGGGTAAAAAATGAGA-TTA
1 AAAAAATTAGGTACTCAATTATAAAGATAAAAAATGAGATTTA
*
947479 AAAAAATTAAAGGT-CTCAATTATAAAGAT-AAAAATGATATTTA
1 AAAAAATT--AGGTACTCAATTATAAAGATAAAAAATGAGATTTA
947522 AAAAAAT
1 AAAAAAT
947529 AAAAAAAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
42 17 0.39
43 23 0.52
44 4 0.09
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (43 bp):
AAAAAATTAGGTACTCAATTATAAAGATAAAAAATGAGATTTA
Found at i:952045 original size:36 final size:36
Alignment explanation
Indices: 951956--952074 Score: 188
Period size: 35 Copynumber: 3.3 Consensus size: 36
951946 TGGCAACCAA
951956 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
951993 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
952028 CTTTGAAAAATAGTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
952064 -GTTGAAAAATG
1 CTTTGAAAAATG
952075 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
35 40 0.52
36 32 0.42
37 5 0.06
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:956616 original size:37 final size:37
Alignment explanation
Indices: 956570--956653 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
956560 TGGCAACCAA
*
956570 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
956607 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
956644 -GTTGAAAAAT
1 CTTTGAAAAAT
956654 GATAATAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 9 0.21
37 34 0.79
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:965048 original size:2 final size:2
Alignment explanation
Indices: 965041--965072 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
965031 TAATCATTCT
965041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
965073 AGAAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:967700 original size:26 final size:26
Alignment explanation
Indices: 967664--967726 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
967654 ATTTTCTATT
967664 TAGGTGTCTAAATTTTTCAGTCAATG
1 TAGGTGTCTAAATTTTTCAGTCAATG
967690 TAGGTGTCTAAATTTTTCAGTCAATG
1 TAGGTGTCTAAATTTTTCAGTCAATG
967716 TAGGTGTCTAA
1 TAGGTGTCTAA
967727 CGTTACGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (26 bp):
TAGGTGTCTAAATTTTTCAGTCAATG
Found at i:969726 original size:2 final size:2
Alignment explanation
Indices: 969719--969818 Score: 66
Period size: 2 Copynumber: 50.0 Consensus size: 2
969709 TAGGAAAGCA
* *
969719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AA AT GAG AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
* * * *
969759 ACT -T AT GACT AT ACC AT AA AT AT TT AA AT -T AT AT AT AT AT AT
1 A-T AT AT -A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
969801 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
969819 TAATTGTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
1 5 0.06
2 67 0.87
3 4 0.05
4 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:975619 original size:2 final size:2
Alignment explanation
Indices: 975612--975645 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
975602 ATTATGTATG
975612 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
975646 GTTATGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:975945 original size:15 final size:15
Alignment explanation
Indices: 975917--975963 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
975907 CCTTTTAAAC
*
975917 AAGTGTAAAATTCAA
1 AAGTGTGAAATTCAA
* *
975932 AAGTTTGAATTTCAA
1 AAGTGTGAAATTCAA
*
975947 ACGTGTGAAATTCAA
1 AAGTGTGAAATTCAA
975962 AA
1 AA
975964 CCAGCAAGAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.30
Consensus pattern (15 bp):
AAGTGTGAAATTCAA
Found at i:982095 original size:6 final size:6
Alignment explanation
Indices: 982086--982147 Score: 97
Period size: 6 Copynumber: 10.3 Consensus size: 6
982076 TTGCTATGAT
* * *
982086 ACATGC ACATGC ACATGC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
982134 ACATAC ACATAC AC
1 ACATAC ACATAC AC
982148 TCTTTCCTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.45, C:0.34, G:0.05, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:985531 original size:3 final size:3
Alignment explanation
Indices: 985525--985549 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
985515 AGATAATAGT
985525 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
985550 CTTGGTGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:989720 original size:13 final size:12
Alignment explanation
Indices: 989693--989719 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
989683 TTCTTTATTA
989693 TTTAAAAAGATT
1 TTTAAAAAGATT
989705 TTTAAAAAGATT
1 TTTAAAAAGATT
989717 TTT
1 TTT
989720 TCCCAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTAAAAAGATT
Found at i:991473 original size:21 final size:21
Alignment explanation
Indices: 991449--991493 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
991439 GTAGTGTGGA
991449 ACTGTAAACACTATCGTGGCT
1 ACTGTAAACACTATCGTGGCT
*
991470 ACTGTAAACACTATCTTGGCT
1 ACTGTAAACACTATCGTGGCT
991491 ACT
1 ACT
991494 CTAGCCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (21 bp):
ACTGTAAACACTATCGTGGCT
Found at i:991519 original size:22 final size:22
Alignment explanation
Indices: 991491--991536 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
991481 TATCTTGGCT
991491 ACTCTAGCCACCAAGAAAGGCA
1 ACTCTAGCCACCAAGAAAGGCA
*
991513 ACTCTAGCCACCAAGAGAGGCA
1 ACTCTAGCCACCAAGAAAGGCA
991535 AC
1 AC
991537 AAGCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.33, G:0.20, T:0.09
Consensus pattern (22 bp):
ACTCTAGCCACCAAGAAAGGCA
Found at i:992416 original size:24 final size:24
Alignment explanation
Indices: 992387--992436 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
992377 TGGTGGTTGA
*
992387 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
992411 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
992435 TT
1 TT
992437 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:992942 original size:17 final size:16
Alignment explanation
Indices: 992911--992944 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
992901 CACGTGAGGA
992911 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
992927 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
992944 T
1 T
992945 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:999337 original size:20 final size:20
Alignment explanation
Indices: 999295--999338 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
999285 TAACTTTTTC
*
999295 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
999315 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
999334 TTTTA
1 TTTTA
999339 CATTTTCTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:1002646 original size:24 final size:24
Alignment explanation
Indices: 1002617--1002666 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1002607 TGGTGGTTGA
*
1002617 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1002641 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1002665 TT
1 TT
1002667 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1003172 original size:17 final size:16
Alignment explanation
Indices: 1003141--1003174 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1003131 CACGTGAGGA
1003141 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1003157 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1003174 T
1 T
1003175 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1006817 original size:405 final size:412
Alignment explanation
Indices: 1006075--1006867 Score: 1431
Period size: 405 Copynumber: 1.9 Consensus size: 412
1006065 CATGTCTCTT
1006075 AAAAAGAATGCCCACGGACTAGGTCAATCTAGTGCTCAAATTTTTAAAAAATTCCAGGCCCAGGC
1 AAAAAGAATGCCCACGGACTAGGTCAATCTAGTGCTCAAATTTTTAAAAAATTCCAGGCCCAGGC
1006140 CTATTCAAATTATCCAGCTCTTTTTTTTATCGTCAATACATGAATAAATTAGCCCATGGGTTAAA
66 CTATTCAAATTATCCAGCTCTTTTTTTTATCGTCAATACATGAATAAATTAGCCCATGGGTTAAA
*
1006205 AAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAATGAGTCGTGTCGAGCTTGACTTAAAT
131 AAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAACGAGTCGTGTCGAGCTTGACTTAAAT
*
1006270 CAAAAACTTTAAAATTAATTTTGATTCAACTCGAAAACTTGCAAGTTTAAAATTGTCAAGCTCTA
196 CAAAAACATTAAAATTAA-TTTGATTCAACTCGAAAACTTGCAAGTTTAAAATTGTCAAGCTCTA
1006335 CTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTTGAAAGCTTATAAGCTTAAAATTTTGA
260 CTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTTGAAAGCTTATAAGCTTAAAATTTTGA
1006400 AGCTCCACTCGAAAT-AAAAAAAAATTAAGTTCGACTCAATCTCGAACACAAACATTAAATACGT
325 AGCTCCACTCGAAATAAAAAAAAAATTAAGTTCGACTCAATCTCGAACACAAACATTAAATACGT
1006464 AAAGACATATTATATATATTTCA
390 AAAGACATATTATATATATTTCA
* *
1006487 AAAAAGAATG-CCATGGACTAGGTCAATCTAGTGCTCAAATTTTTTAGAAAATT-CAGG-CCAGG
1 AAAAAGAATGCCCACGGACTAGGTCAATCTAGTGCTCAAA-TTTTTAAAAAATTCCAGGCCCAGG
* *
1006549 CCTATTCAAATTATCCATCTCTTTTTTTTATCGTCAATACATTAATAAA-TAGCCCATGGGTTAA
65 CCTATTCAAATTATCCAGCTCTTTTTTTTATCGTCAATACATGAATAAATTAGCCCATGGGTTAA
* *
1006613 AAAACTTTATTCATATTTAGTGTGGGCCTAGAGCCGTAAACGAGTCGTGTTGAGCTTGACTTAAA
130 AAAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAACGAGTCGTGTCGAGCTTGACTTAAA
1006678 TCAAAAACATTAAAATTAA-TTGATT-AACTCGAAAAC-TGCAAGTTTAAAATTGTCAAGCTCTA
195 TCAAAAACATTAAAATTAATTTGATTCAACTCGAAAACTTGCAAGTTTAAAATTGTCAAGCTCTA
1006740 CTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTTGAAAGCTTATAAGCTTAAAATTTTGA
260 CTCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTTGAAAGCTTATAAGCTTAAAATTTTGA
1006805 AGCTCCACTCGAAATAAAAAAAAAAATTAAGTTCGACTCAATCTCGAACACAAACATTAAATA
325 AGCTCCACTCGAAAT-AAAAAAAAAATTAAGTTCGACTCAATCTCGAACACAAACATTAAATA
1006868 AAGAATGCCA
Statistics
Matches: 370, Mismatches: 8, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
405 106 0.29
406 11 0.03
407 52 0.14
409 95 0.26
410 52 0.14
411 32 0.09
412 22 0.06
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (412 bp):
AAAAAGAATGCCCACGGACTAGGTCAATCTAGTGCTCAAATTTTTAAAAAATTCCAGGCCCAGGC
CTATTCAAATTATCCAGCTCTTTTTTTTATCGTCAATACATGAATAAATTAGCCCATGGGTTAAA
AAACTTTATTCATATTTAGAGTGGGCCTAGAGCCGTAAACGAGTCGTGTCGAGCTTGACTTAAAT
CAAAAACATTAAAATTAATTTGATTCAACTCGAAAACTTGCAAGTTTAAAATTGTCAAGCTCTAC
TCGATCTCGAAATAAAAAATTAAAGCTCGAATCGACTTGAAAGCTTATAAGCTTAAAATTTTGAA
GCTCCACTCGAAATAAAAAAAAAATTAAGTTCGACTCAATCTCGAACACAAACATTAAATACGTA
AAGACATATTATATATATTTCA
Found at i:1008435 original size:17 final size:17
Alignment explanation
Indices: 1008413--1008446 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1008403 AATCATTCCC
1008413 TTTGTTAAGGTTGCCCG
1 TTTGTTAAGGTTGCCCG
1008430 TTTGTTAAGGTTGCCCG
1 TTTGTTAAGGTTGCCCG
1008447 AAGTGCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (17 bp):
TTTGTTAAGGTTGCCCG
Found at i:1008974 original size:2 final size:2
Alignment explanation
Indices: 1008967--1009002 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1008957 ACTTTTATTC
1008967 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1009003 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1008982 original size:10 final size:9
Alignment explanation
Indices: 1008962--1009002 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
1008952 CCCTTACTTT
1008962 TATTCATATA
1 TATT-ATATA
1008972 TA-TATATA
1 TATTATATA
1008980 TA-TATATA
1 TATTATATA
1008988 TATTAT-TA
1 TATTATATA
1008996 TATTATA
1 TATTATA
1009003 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 23 0.79
9 4 0.14
10 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATATA
Found at i:1018134 original size:2 final size:2
Alignment explanation
Indices: 1018127--1018152 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1018117 AAAATGTGAA
1018127 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
1018153 GGTTTAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1026573 original size:36 final size:36
Alignment explanation
Indices: 1026503--1026574 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
1026493 CTATAATTAA
* *
1026503 TTTATATATTTTCTTTAAAAATTTAAATTCATAAAT
1 TTTATATATTTTCTTTAAAAATTGAAATACATAAAT
*
1026539 TTTATATAATTTT-TTTACAAAATTGAAA-AGATAAAT
1 TTTATAT-ATTTTCTTTA-AAAATTGAAATACATAAAT
1026575 AGGTTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTATATATTTTCTTTAAAAATTGAAATACATAAAT
Found at i:1027765 original size:2 final size:2
Alignment explanation
Indices: 1027758--1027807 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1027748 TACCACAAAC
1027758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1027800 AT AT AT AT
1 AT AT AT AT
1027808 CGGCTTTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1032818 original size:21 final size:20
Alignment explanation
Indices: 1032792--1032889 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
1032782 ATCAGTTTCC
1032792 AAAATCGCAACGCGATTCTTA
1 AAAATCGCAACGCGATT-TTA
* **
1032813 AAAATCGCAATGCGATAGTA
1 AAAATCGCAACGCGATTTTA
* ** *
1032833 CAAATTCGCATTGCGATTTTCC
1 -AAAATCGCAACGCGATTTT-A
* * *
1032855 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTA
1032875 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1032890 ACACATAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTA
Found at i:1032918 original size:20 final size:20
Alignment explanation
Indices: 1032856--1033085 Score: 230
Period size: 20 Copynumber: 11.5 Consensus size: 20
1032846 CGATTTTCCA
* ** *
1032856 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1032876 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1032896 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1032916 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1032936 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1032956 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1032976 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1032996 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
1033016 AAATCACAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1033036 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1033056 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1033076 AAATCACAAC
1 AAATCGCAAC
1033086 ACTGAAATTT
Statistics
Matches: 177, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 174 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1033804 original size:24 final size:24
Alignment explanation
Indices: 1033765--1033811 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1033755 AAATTTGGTC
1033765 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1033789 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1033812 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1034003 original size:12 final size:12
Alignment explanation
Indices: 1033986--1034010 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1033976 ATATAATCCT
1033986 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1033998 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1034010 G
1 G
1034011 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1035897 original size:33 final size:33
Alignment explanation
Indices: 1035793--1035900 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
1035783 CGGAAATTAC
1035793 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1035826 AATCCCAAC-ATGAAAATCGCAATGCAGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
1035860 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1035893 AATCGCAA
1 AATCGCAA
1035901 TGCGAAATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1035898 original size:19 final size:19
Alignment explanation
Indices: 1035807--1035957 Score: 143
Period size: 19 Copynumber: 8.7 Consensus size: 19
1035797 GCAACGAGAG
1035807 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1035826 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1035840 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1035860 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1035874 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1035893 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1035912 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1035926 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1035945 AATCGCATTGCGA
1 AATCGCAATGCGA
1035958 TTCTCTCGTT
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
14 32 0.30
15 2 0.02
16 5 0.05
17 4 0.04
18 3 0.03
19 49 0.45
20 13 0.12
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1035920 original size:52 final size:52
Alignment explanation
Indices: 1035835--1035957 Score: 219
Period size: 52 Copynumber: 2.3 Consensus size: 52
1035825 AAATCCCAAC
1035835 ATGAAAATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1035888 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1035940 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
1035958 TTCTCTCGTT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 52 0.76
53 16 0.24
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1036060 original size:52 final size:53
Alignment explanation
Indices: 1035947--1036063 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1035937 GAAATTAAAA
*
1035947 TCGCATTGCGATTCTCTCGTTGCGATTTTTATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1036000 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1036052 TCGCATTGCGAT
1 TCGCATTGCGAT
1036064 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1036071 original size:19 final size:19
Alignment explanation
Indices: 1035966--1036063 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1035956 GATTCTCTCG
*
1035966 TTGCGATTTTTATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1035986 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1036005 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1036019 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036038 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1036057 TTGCGAT
1 TTGCGAT
1036064 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 36 0.51
20 14 0.20
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1036203 original size:14 final size:14
Alignment explanation
Indices: 1036170--1036205 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1036160 CATCAATTAC
1036170 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1036184 -CAAATCATCTTTT
1 ACAAATCAACTTTT
1036197 ACAAATCAA
1 ACAAATCAA
1036206 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1038160 original size:19 final size:19
Alignment explanation
Indices: 1038118--1038290 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
1038108 TAGTTTACTT
* *
1038118 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1038138 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
1038157 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
1038176 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1038195 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1038214 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1038228 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1038247 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1038261 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1038280 TCGCAATGCGA
1 TCGCAACGCGA
1038291 TTTTGGTTTC
Statistics
Matches: 130, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
14 16 0.12
16 11 0.08
17 11 0.08
19 80 0.62
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1038231 original size:14 final size:14
Alignment explanation
Indices: 1038212--1038268 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1038202 GCGAAATGAA
*
1038212 AATCGCAACGACAG
1 AATCGCAACGAAAG
1038226 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1038243 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1038259 AATCGCAACG
1 AATCGCAACG
1038269 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1038239 original size:33 final size:33
Alignment explanation
Indices: 1038193--1038285 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1038183 GCGAAACCAA
*
1038193 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1038226 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1038259 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1038286 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1038308 original size:19 final size:19
Alignment explanation
Indices: 1038286--1038414 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1038276 AAAATCGCAA
1038286 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1038305 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1038319 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1038338 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1038352 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1038371 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1038390 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1038410 TGCGA
1 TGCGA
1038415 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1038328 original size:33 final size:33
Alignment explanation
Indices: 1038286--1038377 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1038276 AAAATCGCAA
1038286 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1038319 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1038352 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1038378 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1038578 original size:93 final size:93
Alignment explanation
Indices: 1038462--1039115 Score: 1267
Period size: 93 Copynumber: 7.1 Consensus size: 93
1038452 ATGGATTGCA
1038462 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1038526 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1038554 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1038619 TAGCAGAATTAGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1038647 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1038712 TAGCAGAATTGGCAGCAATCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1038740 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1038805 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1038833 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1038898 TAGCAGAATTGGCAGCAACCGAAC-AAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1038925 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1038990 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1039018 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1039083 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1039111 TTACT
1 TTACT
1039116 AAGCAATCTA
Statistics
Matches: 555, Mismatches: 5, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
92 96 0.17
93 459 0.83
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1039100 original size:278 final size:279
Alignment explanation
Indices: 1038462--1039115 Score: 1267
Period size: 278 Copynumber: 2.4 Consensus size: 279
1038452 ATGGATTGCA
1038462 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1038526 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1038591 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTAGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTAGCAGCAACCGAACAAATTTACTTTCA
1038656 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
*
1038721 TGGCAGCAATCGAACAAAT
261 TGGCAGCAACCGAACAAAT
1038740 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1038805 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
1038870 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC-AATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTAGCAGCAACCGAACAAATTTACTTTCA
1038934 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
1038999 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
1039018 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1039083 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
1039116 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
278 196 0.53
279 176 0.47
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTAGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:1040844 original size:20 final size:20
Alignment explanation
Indices: 1040813--1040876 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1040803 TTTTGGTTGA
1040813 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1040833 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1040853 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
1040874 AAT
1 AAT
1040877 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1040865 original size:21 final size:21
Alignment explanation
Indices: 1040811--1040875 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1040801 TCTTTTGGTT
1040811 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1040832 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1040852 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1040873 GAA
1 GAA
1040876 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1040936 original size:14 final size:14
Alignment explanation
Indices: 1040917--1040973 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1040907 TTTGGTTTCG
1040917 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1040931 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1040950 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1040964 CGTTGCGATT
1 CGTTGCGATT
1040974 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1040949 original size:33 final size:33
Alignment explanation
Indices: 1040901--1040981 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1040891 AAAATCGCAA
**
1040901 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1040934 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1040967 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1040982 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1040984 original size:21 final size:21
Alignment explanation
Indices: 1040958--1041033 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1040948 CGCGTTGCGA
1040958 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1040979 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1040999 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* *
1041020 TTATCTTGTTGCGA
1 TTCTCTCGTTGCGA
1041034 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1041014 original size:41 final size:41
Alignment explanation
Indices: 1040957--1041034 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1040947 TCGCGTTGCG
*
1040957 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
*
1040998 ATTCTCTCGTTGCGATTTTCATTTATCTTGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1041035 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1041155 original size:33 final size:33
Alignment explanation
Indices: 1041113--1041183 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1041103 AATACTAACT
*
1041113 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1041146 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1041179 TGAAA
1 TGAAA
1041184 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1041590 original size:20 final size:20
Alignment explanation
Indices: 1041565--1041758 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1041555 CTTTAAATAT
1041565 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1041585 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1041607 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1041626 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1041646 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1041666 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1041686 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1041706 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1041726 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1041746 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1041759 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1041752 original size:60 final size:60
Alignment explanation
Indices: 1041565--1041758 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1041555 CTTTAAATAT
**
1041565 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1041626 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1041686 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1041746 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1041759 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1041775 original size:21 final size:21
Alignment explanation
Indices: 1041745--1041827 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1041735 ATTTTCATAT
*
1041745 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1041766 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1041787 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1041808 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1041828 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1041818 original size:42 final size:43
Alignment explanation
Indices: 1041725--1041823 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1041715 ATTTATGTGT
* *
1041725 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1041766 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1041808 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1041824 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1042982 original size:55 final size:56
Alignment explanation
Indices: 1042915--1043027 Score: 174
Period size: 55 Copynumber: 2.0 Consensus size: 56
1042905 TTTCCTCGAT
* * *
1042915 CAGGTAGGTTTAAATATAATATTTATTTCATAG-AAAATACCTTAAATAAATTTAA
1 CAGGTAAGTTTAAATATAATATTAATTTCATAGAAAAATACCTCAAATAAATTTAA
* *
1042970 CAGGTAAGTTTAAATATAATATTAATTTCATCGAAAAATACCTCAAATAGATTTAA
1 CAGGTAAGTTTAAATATAATATTAATTTCATAGAAAAATACCTCAAATAAATTTAA
1043026 CA
1 CA
1043028 TGGGACTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
55 30 0.58
56 22 0.42
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (56 bp):
CAGGTAAGTTTAAATATAATATTAATTTCATAGAAAAATACCTCAAATAAATTTAA
Found at i:1047006 original size:14 final size:14
Alignment explanation
Indices: 1046987--1047017 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1046977 AGATTTATTG
1046987 AAAATAAAAAAATA
1 AAAATAAAAAAATA
1047001 AAAATAAAAAAATA
1 AAAATAAAAAAATA
1047015 AAA
1 AAA
1047018 GGATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:1047023 original size:22 final size:23
Alignment explanation
Indices: 1046987--1047030 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1046977 AGATTTATTG
1046987 AAAATAAAAAAATAA-AAATAAA
1 AAAATAAAAAAATAATAAATAAA
**
1047009 AAAATAAAAGGATAATAAATAA
1 AAAATAAAAAAATAATAAATAA
1047031 TACCGGTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAATAAAAAAATAATAAATAAA
Found at i:1052495 original size:227 final size:226
Alignment explanation
Indices: 1052096--1052542 Score: 788
Period size: 227 Copynumber: 2.0 Consensus size: 226
1052086 GTAAATTATC
* * *
1052096 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1052161 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
1052226 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATTG
1052290 AAACATAAATTACATAACTTTCAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAGTATA
*
1052322 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1052387 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
*
1052452 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
1052517 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
1052543 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
226 36 0.17
227 147 0.70
228 27 0.13
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAGTATA
Found at i:1054461 original size:23 final size:23
Alignment explanation
Indices: 1054430--1054492 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1054420 ATAGGTAAAC
*
1054430 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1054453 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1054476 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1054493 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1054500 original size:23 final size:23
Alignment explanation
Indices: 1054430--1054502 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1054420 ATAGGTAAAC
* * **
1054430 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1054453 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1054476 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1054499 ATAT
1 ATAT
1054503 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1061442 original size:33 final size:33
Alignment explanation
Indices: 1061403--1061479 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
1061393 AATTCTCATC
* *
1061403 ATTTTATTTGGGTATGTAAATCTACGAGTATTT
1 ATTTTATTTGGGTATGTAAATATACGAGTAATT
*
1061436 ATTTTATTTGGGTATGTAAATATAGGAGTAATT
1 ATTTTATTTGGGTATGTAAATATACGAGTAATT
* *
1061469 ACTTCATTTGG
1 ATTTTATTTGG
1061480 TAAGCATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTTATTTGGGTATGTAAATATACGAGTAATT
Found at i:1066091 original size:20 final size:22
Alignment explanation
Indices: 1066066--1066108 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1066056 ATGGCTCGAT
1066066 AAAAATTAAAT-CAATC-AAAA
1 AAAAATTAAATCCAATCTAAAA
*
1066086 AAAAATTTAATCCAATCTAAAA
1 AAAAATTAAATCCAATCTAAAA
1066108 A
1 A
1066109 TTAATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAATTAAATCCAATCTAAAA
Found at i:1081402 original size:30 final size:30
Alignment explanation
Indices: 1081363--1081443 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
1081353 GATCTCTAAA
* *
1081363 TTTAAATAAAATATTAATTTAACTT-TGATT
1 TTTAGATAAAATATTAATTTAA-TTATGAAT
*
1081393 TTTAGATAAAATACTAATTTAATTCATGAAT
1 TTTAGATAAAATATTAATTTAATT-ATGAAT
1081424 TTTAGATAAAAAATATTAAT
1 TTTAGAT--AAAATATTAAT
1081444 ATCATCCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 20 0.47
31 11 0.26
33 10 0.23
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTAGATAAAATATTAATTTAATTATGAAT
Found at i:1082919 original size:23 final size:23
Alignment explanation
Indices: 1082893--1082953 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1082883 TAAACGGGAT
*
1082893 TTAAATGAAAATGTTTACGAACG
1 TTAAATGAAAATGTTTACGAACA
*
1082916 TTAAAT-AAATATGTTTATGAACA
1 TTAAATGAAA-ATGTTTACGAACA
*
1082939 TTAAATGAACATGTT
1 TTAAATGAAAATGTT
1082954 AGCACACGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.09
23 28 0.85
24 2 0.06
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (23 bp):
TTAAATGAAAATGTTTACGAACA
Found at i:1083325 original size:30 final size:31
Alignment explanation
Indices: 1083291--1083350 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1083281 ATTTAATGAT
*
1083291 CAAAATGTAAT-AATTAATAACATAAGTGAA
1 CAAAATGTAATAAATCAATAACATAAGTGAA
* *
1083321 CAAAATTTAATAAATCAATAACGTAAGTGA
1 CAAAATGTAATAAATCAATAACATAAGTGA
1083351 TTGAAACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (31 bp):
CAAAATGTAATAAATCAATAACATAAGTGAA
Found at i:1084179 original size:60 final size:59
Alignment explanation
Indices: 1084036--1084180 Score: 143
Period size: 60 Copynumber: 2.4 Consensus size: 59
1084026 TTTTTGGGTG
* * *
1084036 AAGTATAC-AAATGATCCTCTAACTATAGGTATTGTTTTATTAAGTCACATGACTATTGA
1 AAGT-TACAAAATGATCATCTGACTATAGGTATTGTTTTATTAAGTCACATGACTATTAA
* * * * **
1084095 AAGTTATAAAATAATCCATC-GACTATAAGGTATTGTTTTGTTGAGTC-TGTCGACTATTAA
1 AAGTTACAAAATGAT-CATCTGACTAT-AGGTATTGTTTTATTAAGTCACAT-GACTATTAA
*
1084155 AAGTTACAAAATGATCGTCTGACTAT
1 AAGTTACAAAATGATCATCTGACTAT
1084181 TTACATGTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
58 2 0.03
59 19 0.28
60 48 0.70
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (59 bp):
AAGTTACAAAATGATCATCTGACTATAGGTATTGTTTTATTAAGTCACATGACTATTAA
Found at i:1087060 original size:11 final size:11
Alignment explanation
Indices: 1087046--1087078 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1087036 ATGCTAACGG
1087046 TATTATTTCCT
1 TATTATTTCCT
1087057 TATTATTTCCT
1 TATTATTTCCT
*
1087068 TATTCTTTCCT
1 TATTATTTCCT
1087079 CGTATCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATTTCCT
Found at i:1088658 original size:18 final size:18
Alignment explanation
Indices: 1088595--1088658 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 18
1088585 TAATATTTCT
*
1088595 TTTTTAATATTTTAATAC
1 TTTTTAATATTTTAATAA
**
1088613 TTTTTTGTATTTTAAT-A
1 TTTTTAATATTTTAATAA
* *
1088630 TTTTGAAT-TTTAAATAA
1 TTTTTAATATTTTAATAA
1088647 TTTTTAAT-TTTT
1 TTTTTAATATTTT
1088659 TTATTTAGAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 6 0.17
17 16 0.44
18 14 0.39
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAATATTTTAATAA
Found at i:1088718 original size:30 final size:30
Alignment explanation
Indices: 1088682--1088738 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1088672 ATAAAAAATT
*
1088682 AAACTTTCTAAAAGAAACAATTAAGTTGTC
1 AAACTTTATAAAAGAAACAATTAAGTTGTC
**
1088712 AAACTTTATAAAAGAATTAATTAAGTT
1 AAACTTTATAAAAGAAACAATTAAGTT
1088739 TATCTATCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (30 bp):
AAACTTTATAAAAGAAACAATTAAGTTGTC
Found at i:1103856 original size:36 final size:37
Alignment explanation
Indices: 1103785--1103869 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
1103775 ATCCCATTAT
*
1103785 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
1103821 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
1103857 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1103870 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:1108427 original size:36 final size:37
Alignment explanation
Indices: 1108356--1108440 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
1108346 ATCCCATTAT
*
1108356 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
1108392 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
1108428 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1108441 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:1108937 original size:31 final size:30
Alignment explanation
Indices: 1108899--1108963 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 30
1108889 CAATTAATCC
1108899 GGGACCATATTGCAAACGGACTAAATGTTG
1 GGGACCATATTGCAAACGGACTAAATGTTG
*
1108929 AGGGACCATATTTCAAACGGACTAAATGTTG
1 -GGGACCATATTGCAAACGGACTAAATGTTG
1108960 GGGA
1 GGGA
1108964 ATTGTATTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (30 bp):
GGGACCATATTGCAAACGGACTAAATGTTG
Found at i:1111148 original size:31 final size:31
Alignment explanation
Indices: 1111075--1111148 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
1111065 AGTTACATCG
*
1111075 GGGACCATATTACAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
*
1111106 GGGACCATATTGCAAATGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
*
1111137 GGGATCATATTG
1 GGGACCATATTG
1111149 TAAGTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.26
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:1112880 original size:99 final size:100
Alignment explanation
Indices: 1112648--1112941 Score: 405
Period size: 99 Copynumber: 3.0 Consensus size: 100
1112638 AAAAATCAAC
*
1112648 GGTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAATAGCTAGT
1 GGTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAATAACTAGT
* *
1112713 TTAACGTAATATGTTGCGTCTATTTTATTTTAACT
66 TTAACGAAATATGTTGCGCCTATTTTATTTTAACT
* * * **
1112748 GATTAAGTTATAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGGTAACTAGT
1 GGTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAATAACTAGT
*
1112813 TTAAC-AAATATGTTTCGCCTATTTTATTTTAACT
66 TTAACGAAATATGTTGCGCCTATTTTATTTTAACT
* * * * * *
1112847 GGTTAAGTTGTAAATATTTTATCATTTACATTATTATTATACATTTAAACAAACCGACAGCTAGT
1 GGTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAATAACTAGT
* * *
1112912 TTAACGTAATAGGTT--GTCTATTTTATTTTA
66 TTAACGAAATATGTTGCGCCTATTTTATTTTA
1112942 CCTTTTACAT
Statistics
Matches: 172, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
98 14 0.08
99 87 0.51
100 71 0.41
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (100 bp):
GGTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCAATAACTAGT
TTAACGAAATATGTTGCGCCTATTTTATTTTAACT
Found at i:1112952 original size:74 final size:73
Alignment explanation
Indices: 1112861--1113090 Score: 254
Period size: 74 Copynumber: 3.1 Consensus size: 73
1112851 AAGTTGTAAA
* *
1112861 TATTTTATCATTTACATTATTATTATACATTTAAACAAACCGACAGCTAGTTTAACGTAATAGGT
1 TATTTTACCATTTACATTATTATTATACATTTAAACAAACC-ATAGCTAGTTTAACGTAATAGGT
1112926 TGTCTATTT
65 TGTCTATTT
* * * * **
1112935 TATTTTACCTTTTACATTATTGTTATACTTTTAAACAAACCAGTAGCTAGTTTAATGTAATAATT
1 TATTTTACCATTTACATTATTATTATACATTTAAACAAACCA-TAGCTAGTTTAACGTAATAGGT
1113000 TGTGCCTATTT
65 TGT--CTATTT
*
1113011 TA--TT--CAGTTTACATTATTATTATACCTTTAAACAAA-CATATGACTAGTTTAACGTAATAG
1 TATTTTACCA-TTTACATTATTATTATACATTTAAACAAACCATA-G-CTAGTTTAACGTAATAG
*
1113071 GTTGCACCTATTT
63 GTTG--TCTATTT
1113084 TATTTTA
1 TATTTTA
1113091 ACCGGTTAAT
Statistics
Matches: 130, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
71 2 0.02
72 4 0.03
73 54 0.42
74 60 0.46
75 2 0.02
76 8 0.06
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (73 bp):
TATTTTACCATTTACATTATTATTATACATTTAAACAAACCATAGCTAGTTTAACGTAATAGGTT
GTCTATTT
Found at i:1113058 original size:73 final size:70
Alignment explanation
Indices: 1112861--1113087 Score: 253
Period size: 73 Copynumber: 3.1 Consensus size: 70
1112851 AAGTTGTAAA
*
1112861 TATTTTA-TCATTTACATTATTATTATACATTTAAACAAACCGACAGCTAGTTTAACGTAATAGG
1 TATTTTATTCATTTACATTATTATTATACATTTAAACAAACC-ATAGCTAGTTTAACGTAATAGG
1112925 TTGT-C
65 TTGTCC
* * * *
1112930 TATTTTATTTTACCTTTTACATTATTGTTATACTTTTAAACAAACCAGTAGCTAGTTTAATGTAA
1 TATTTTA--TT--CATTTACATTATTATTATACATTTAAACAAACCA-TAGCTAGTTTAACGTAA
**
1112995 TAATTTGTGCC
61 TAGGTTGT-CC
*
1113006 TATTTTATTCAGTTTACATTATTATTATACCTTTAAACAAA-CATATGACTAGTTTAACGTAATA
1 TATTTTATTCA-TTTACATTATTATTATACATTTAAACAAACCATA-G-CTAGTTTAACGTAATA
*
1113070 GGTTGCACC
63 GGTTG-TCC
1113079 TATTTTATT
1 TATTTTATT
1113088 TTAACCGGTT
Statistics
Matches: 132, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
69 7 0.05
71 2 0.02
72 5 0.04
73 57 0.43
74 53 0.40
76 8 0.06
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (70 bp):
TATTTTATTCATTTACATTATTATTATACATTTAAACAAACCATAGCTAGTTTAACGTAATAGGT
TGTCC
Found at i:1113203 original size:76 final size:76
Alignment explanation
Indices: 1113108--1113266 Score: 212
Period size: 76 Copynumber: 2.1 Consensus size: 76
1113098 AATTTGTAAA
* * **
1113108 TATTTTGTTGTTTACATTATTATTATATATTTAAACAAATCACTAGATAGTTTAACT-TAATATG
1 TATTTTATCGTTTACATTATTATTATATATTTAAACAAATCACTAGATAGTTTAA-TGTAATACA
* *
1113172 TTGCGTTTATTT
65 TTGCATGTATTT
* ** *
1113184 TATTTTATCGTTTACATTATTATTATATCTTTAAACAAATCGGTAGCTAGTTTAATGTAATACAT
1 TATTTTATCGTTTACATTATTATTATATATTTAAACAAATCACTAGATAGTTTAATGTAATACAT
1113249 TGCATGTATTT
66 TGCATGTATTT
1113260 TATTTTA
1 TATTTTA
1113267 ACCGGTTAAG
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 1 0.01
76 71 0.99
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.50
Consensus pattern (76 bp):
TATTTTATCGTTTACATTATTATTATATATTTAAACAAATCACTAGATAGTTTAATGTAATACAT
TGCATGTATTT
Found at i:1115766 original size:83 final size:83
Alignment explanation
Indices: 1115539--1115788 Score: 403
Period size: 82 Copynumber: 3.0 Consensus size: 83
1115529 ACCAAATTAC
* *
1115539 AAGTATTTAATACTAATTTCATAACATGTCACATCATCAAATTAGGTATAACCGTTTTTGAGATA
1 AAGTATTTAATACTAATTCCATAACATGTGACATCATCAAATTAGGTATAACCGTTTTTGAGATA
1115604 AAACTAATAGTTTAATAA
66 AAACTAATAGTTTAATAA
* * *
1115622 AAGTA-TTAGTACTAATTCCATAACATGTGATATCATCAAATTAGGTATAACCGTTTTTGAGATC
1 AAGTATTTAATACTAATTCCATAACATGTGACATCATCAAATTAGGTATAACCGTTTTTGAGATA
1115686 AAACTAATAGTTTAATAA
66 AAACTAATAGTTTAATAA
* * *
1115704 AAGTATTTAATACTAATTCCATAACATGTGACCTCATCAAATTAGGTATAACAGTTTTTGAGATT
1 AAGTATTTAATACTAATTCCATAACATGTGACATCATCAAATTAGGTATAACCGTTTTTGAGATA
* *
1115769 AAACTAAAAGTTAAATAA
66 AAACTAATAGTTTAATAA
1115787 AA
1 AA
1115789 AATAGAAAAC
Statistics
Matches: 154, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
82 77 0.50
83 77 0.50
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (83 bp):
AAGTATTTAATACTAATTCCATAACATGTGACATCATCAAATTAGGTATAACCGTTTTTGAGATA
AAACTAATAGTTTAATAA
Found at i:1120480 original size:14 final size:14
Alignment explanation
Indices: 1120459--1120502 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1120449 AAATTAAATT
1120459 AATATTTAAAAAAA
1 AATATTTAAAAAAA
**
1120473 CTTATTTAAAAAAA
1 AATATTTAAAAAAA
*
1120487 AAAATTTAAAAAAA
1 AATATTTAAAAAAA
1120501 AA
1 AA
1120503 AACTCAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
AATATTTAAAAAAA
Found at i:1120757 original size:16 final size:17
Alignment explanation
Indices: 1120726--1120758 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1120716 TAAATTAATA
*
1120726 TTTAAAAAAACTTATTT
1 TTTAAAAAAACATATTT
1120743 TTTAAAAAAA-ATATTT
1 TTTAAAAAAACATATTT
1120759 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAAAAAACATATTT
Found at i:1121173 original size:21 final size:22
Alignment explanation
Indices: 1121139--1121182 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1121129 AATTAGGGAT
*
1121139 TTTTTTAATGATAATATTGTTAA
1 TTTTTTAA-GATAAAATTGTTAA
*
1121162 TTTTTTAA-ATAAAATTTTTAA
1 TTTTTTAAGATAAAATTGTTAA
1121183 AATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTTTTAAGATAAAATTGTTAA
Found at i:1126980 original size:28 final size:28
Alignment explanation
Indices: 1126940--1126997 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1126930 TGGATGTAAG
1126940 TTACCTACGTTACTCTTAACTCTTCATT
1 TTACCTACGTTACTCTTAACTCTTCATT
1126968 TTACCTACGTTACTCTTAACTCTTCATT
1 TTACCTACGTTACTCTTAACTCTTCATT
1126996 TT
1 TT
1126998 TCCTTAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.03, T:0.48
Consensus pattern (28 bp):
TTACCTACGTTACTCTTAACTCTTCATT
Found at i:1130990 original size:15 final size:15
Alignment explanation
Indices: 1130970--1130999 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1130960 TTAAATTAAT
*
1130970 TTATAAAATAGTAAA
1 TTATAAAATACTAAA
1130985 TTATAAAATACTAAA
1 TTATAAAATACTAAA
1131000 CATATAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (15 bp):
TTATAAAATACTAAA
Found at i:1146474 original size:28 final size:28
Alignment explanation
Indices: 1146434--1146487 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1146424 GCTGATGTCA
1146434 TGGAAAAAGCTTAACTTGTTATTGTTCG
1 TGGAAAAAGCTTAACTTGTTATTGTTCG
1146462 TGGAAAAAGCTTAACTTGTTATTGTT
1 TGGAAAAAGCTTAACTTGTTATTGTT
1146488 GCTATTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (28 bp):
TGGAAAAAGCTTAACTTGTTATTGTTCG
Found at i:1167895 original size:221 final size:221
Alignment explanation
Indices: 1167510--1167947 Score: 779
Period size: 221 Copynumber: 2.0 Consensus size: 221
1167500 GTGGAACCGT
1167510 ATGTCACATATGGGTATGGAGGCAACCTTTGTTTCTTTCAACTTCCCCTTTTTCTTTTTCCTGGT
1 ATGTCACATATGGGTATGGAGGCAACCTTTGTTTCTTTCAACTTCCCCTTTTTCTTTTTCCTGGT
* *
1167575 AAATGTAAAATGGTGAATCTAATTTTGTGAAAACTTGTATAAATTTTAATGTGTTCCTTCATGTG
66 AAATGTAAAATGGTGAATCCAATTTTGTGAAAACTTGTATAAATTTTAATGTGTTCCTCCATGTG
* *
1167640 TGTCGATGATTTTTTCCTCTAGTATATGCGTATCGTCATTTTATCAGTGCCCACTTTAATAGCCT
131 TGTCGATGATTTTTTCCTCTAGTATATGCGTATCGTCATTTTATCAATGCCCACTTTAATAGCCC
*
1167705 TCAACTTCTTATAGGGCATGTGCCGA
196 TCAACTTCTTATAGGACATGTGCCGA
1167731 ATGTCACATATGGGTATGGAGGCAACCTTTGTTTCTTTCAACTTCCCCTTTTTCTTTTTCCTGGT
1 ATGTCACATATGGGTATGGAGGCAACCTTTGTTTCTTTCAACTTCCCCTTTTTCTTTTTCCTGGT
1167796 AAATGTAAAATGGTGAATCCAATTTTGTGAAAACTTGTATAAATTTTAATGTGTTCCTCCATGTG
66 AAATGTAAAATGGTGAATCCAATTTTGTGAAAACTTGTATAAATTTTAATGTGTTCCTCCATGTG
* * * *
1167861 TGTTGATGCTTTTCTTCCTCTAGTATAT-CGTATCGTCGTTTTATCAATGCCTACTTTAATAGCC
131 TGTCGATGATTTT-TTCCTCTAGTATATGCGTATCGTCATTTTATCAATGCCCACTTTAATAGCC
1167925 CTCAACTTCTTATAGGACATGTG
195 CTCAACTTCTTATAGGACATGTG
1167948 TAACCATTGC
Statistics
Matches: 207, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
221 193 0.93
222 14 0.07
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (221 bp):
ATGTCACATATGGGTATGGAGGCAACCTTTGTTTCTTTCAACTTCCCCTTTTTCTTTTTCCTGGT
AAATGTAAAATGGTGAATCCAATTTTGTGAAAACTTGTATAAATTTTAATGTGTTCCTCCATGTG
TGTCGATGATTTTTTCCTCTAGTATATGCGTATCGTCATTTTATCAATGCCCACTTTAATAGCCC
TCAACTTCTTATAGGACATGTGCCGA
Found at i:1174928 original size:13 final size:13
Alignment explanation
Indices: 1174910--1174954 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1174900 TGATAAATAA
*
1174910 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
1174923 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
1174936 AAACAACTACAAT
1 AAAAAACTACAAT
1174949 AAAAAA
1 AAAAAA
1174955 ACACTAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:1177675 original size:31 final size:31
Alignment explanation
Indices: 1177640--1177710 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1177630 AAAAACGCCA
* *
1177640 ATTTTGTAATGGTTGATAAAATTTAATGATC
1 ATTTTGTAATCGTTGAGAAAATTTAATGATC
* *
1177671 ATTTTGTAATCGTTTAGAAAATTTAATGATT
1 ATTTTGTAATCGTTGAGAAAATTTAATGATC
1177702 ATTTTGTAA
1 ATTTTGTAA
1177711 CTTCTAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTTTGTAATCGTTGAGAAAATTTAATGATC
Found at i:1177791 original size:32 final size:31
Alignment explanation
Indices: 1177750--1177881 Score: 110
Period size: 31 Copynumber: 4.3 Consensus size: 31
1177740 ATTTTAACAT
* * * *
1177750 AATTTAATGATAATTTGTGTACTCTATCCTAA
1 AATTTAATGATAATTT-TATAATATATCATAA
*
1177782 AATTTAATGATCATTTTATAATATATCATAA
1 AATTTAATGATAATTTTATAATATATCATAA
* *
1177813 ATTTTAATGACAATTTTATAATAT-TCTATAA
1 AATTTAATGATAATTTTATAATATATC-ATAA
* ** * *
1177844 AA-TTAATAATCGTCTTATAATAT-TTA-AA
1 AATTTAATGATAATTTTATAATATATCATAA
1177872 AATTTAATGA
1 AATTTAATGA
1177882 CTAAAATGAT
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
28 4 0.05
29 7 0.09
30 19 0.23
31 37 0.45
32 15 0.18
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (31 bp):
AATTTAATGATAATTTTATAATATATCATAA
Found at i:1178592 original size:16 final size:16
Alignment explanation
Indices: 1178571--1178605 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1178561 AAATACTATA
*
1178571 TATATATTTATGTATG
1 TATATATGTATGTATG
1178587 TATATATGTATGTATG
1 TATATATGTATGTATG
1178603 TAT
1 TAT
1178606 TACAAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (16 bp):
TATATATGTATGTATG
Found at i:1178832 original size:15 final size:15
Alignment explanation
Indices: 1178812--1178845 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1178802 TACGTTCATA
*
1178812 ATTTTAGATTTTAAG
1 ATTTTAAATTTTAAG
1178827 ATTTTAAATTTTAAG
1 ATTTTAAATTTTAAG
1178842 ATTT
1 ATTT
1178846 ATGATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
ATTTTAAATTTTAAG
Found at i:1178846 original size:7 final size:8
Alignment explanation
Indices: 1178812--1178845 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
1178802 TACGTTCATA
1178812 ATTTT-AG
1 ATTTTAAG
1178819 ATTTTAAG
1 ATTTTAAG
1178827 ATTTTAA-
1 ATTTTAAG
1178834 ATTTTAAG
1 ATTTTAAG
1178842 ATTT
1 ATTT
1178846 ATGATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 12 0.48
8 13 0.52
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (8 bp):
ATTTTAAG
Done.