Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_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: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:783173 original size:22 final size:24
Alignment explanation
Indices: 783142--783191 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
783132 TGTATATCAT
* * *
783142 ATAACACATATATCATTTCATA-A
1 ATAACACATACATAATATCATATA
783165 ATAA-ACATACATAATATCATATA
1 ATAACACATACATAATATCATATA
783188 ATAA
1 ATAA
783192 TGCAAAGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAACACATACATAATATCATATA
Found at i:783350 original size:22 final size:22
Alignment explanation
Indices: 783325--783366 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
783315 TATGAAATTT
*
783325 TGTCCCGAAGGACCTGTGAATA
1 TGTCCCGAAGGACCTATGAATA
783347 TGTCCCGAAGGACCTATGAA
1 TGTCCCGAAGGACCTATGAA
783367 ACCCTCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGAATA
Found at i:784860 original size:3 final size:3
Alignment explanation
Indices: 784852--784894 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
784842 TCTCTCTCGT
* * * *
784852 ATG ATG ATG ATG ATG AAG AAG AAG AAG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
784895 AATAATTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (3 bp):
ATG
Found at i:785980 original size:30 final size:31
Alignment explanation
Indices: 785935--785992 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
785925 GTAACTTCTG
*
785935 TTTATTTATGTTTATTAAATTAATTTTTATA
1 TTTATTTATGCTTATTAAATTAATTTTTATA
*
785966 TTTA-TTATGCTTATTCAATTAATTTTT
1 TTTATTTATGCTTATTAAATTAATTTTT
785993 CTGTATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTATTTATGCTTATTAAATTAATTTTTATA
Found at i:786274 original size:20 final size:20
Alignment explanation
Indices: 786249--786288 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
786239 TTGCCTATTG
786249 GTTGTTGCC-GCTTGCTGCCT
1 GTTGTTGCCTG-TTGCTGCCT
786269 GTTGTTGCCTGTTGCTGCCT
1 GTTGTTGCCTGTTGCTGCCT
786289 TGTAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.00, C:0.28, G:0.30, T:0.42
Consensus pattern (20 bp):
GTTGTTGCCTGTTGCTGCCT
Found at i:786922 original size:14 final size:14
Alignment explanation
Indices: 786883--786922 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
786873 GATTATATTG
* *
786883 AAGATTTATAACAT
1 AAGAATTATAATAT
*
786897 AAGAATCATAATAT
1 AAGAATTATAATAT
786911 AAGAATTATAAT
1 AAGAATTATAAT
786923 TAATATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (14 bp):
AAGAATTATAATAT
Found at i:787095 original size:16 final size:16
Alignment explanation
Indices: 787070--787106 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
787060 CAATGGTAAT
787070 ATAT-AAGTCAGATAA
1 ATATCAAGTCAGATAA
*
787085 ATATCAAGTCAGGTAA
1 ATATCAAGTCAGATAA
787101 ATATCA
1 ATATCA
787107 TATTAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (16 bp):
ATATCAAGTCAGATAA
Found at i:789879 original size:17 final size:18
Alignment explanation
Indices: 789859--789922 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 18
789849 TTACCTAACG
789859 TTTAGT-TTTTGTTTCGT
1 TTTAGTATTTTGTTTCGT
* *
789876 TTTAGTATTTCGCTAAT-G-
1 TTTAGTATTTTG-T-TTCGT
789894 TTTAGT-TTTTGTTTCGT
1 TTTAGTATTTTGTTTCGT
789911 TTTAGTATTTTG
1 TTTAGTATTTTG
789923 CATTAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
15 1 0.03
16 2 0.05
17 16 0.43
18 15 0.41
19 2 0.05
20 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.17, T:0.64
Consensus pattern (18 bp):
TTTAGTATTTTGTTTCGT
Found at i:789897 original size:35 final size:35
Alignment explanation
Indices: 789853--789920 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
789843 AAAATTTTAC
789853 CTAACGTTTAGTTTTTGTTTCGTTTTAGTATTTCG
1 CTAACGTTTAGTTTTTGTTTCGTTTTAGTATTTCG
*
789888 CTAATGTTTAGTTTTTGTTTCGTTTTAGTATTT
1 CTAACGTTTAGTTTTTGTTTCGTTTTAGTATTT
789921 TGCATTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.15, C:0.09, G:0.16, T:0.60
Consensus pattern (35 bp):
CTAACGTTTAGTTTTTGTTTCGTTTTAGTATTTCG
Found at i:793982 original size:3 final size:3
Alignment explanation
Indices: 793974--794015 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
793964 TAAGTGTTCC
*
793974 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
794016 TGTTCTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:795139 original size:2 final size:2
Alignment explanation
Indices: 795132--795164 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
795122 ACGTGCTAGT
795132 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
795165 CCATGCAAAT
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:795352 original size:2 final size:2
Alignment explanation
Indices: 795345--795383 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
795335 AAGACTTGAT
795345 TA TA TA 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 TA TA TA T
795384 TAATAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:800350 original size:23 final size:23
Alignment explanation
Indices: 800306--800350 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
800296 ATTGACTAAT
* ** *
800306 TTATAAAATTTTAGGTGGTGAAC
1 TTATAAAAGTTTAGAAGATGAAC
800329 TTATAAAAGTTTAGAAGATGAA
1 TTATAAAAGTTTAGAAGATGAA
800351 AATAATTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (23 bp):
TTATAAAAGTTTAGAAGATGAAC
Found at i:801757 original size:13 final size:13
Alignment explanation
Indices: 801739--801763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
801729 TATCTATTAT
801739 TGTATTTATTTTA
1 TGTATTTATTTTA
801752 TGTATTTATTTT
1 TGTATTTATTTT
801764 TTATTAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TGTATTTATTTTA
Found at i:801917 original size:13 final size:13
Alignment explanation
Indices: 801884--801908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
801874 TTTTATATAA
801884 TATATTTATTTTC
1 TATATTTATTTTC
801897 TATATTTATTTT
1 TATATTTATTTT
801909 TTAGTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TATATTTATTTTC
Found at i:804184 original size:2 final size:2
Alignment explanation
Indices: 804177--804204 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
804167 TCTATTATTA
804177 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
804205 TCATTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:804921 original size:22 final size:22
Alignment explanation
Indices: 804895--804937 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
804885 ACATCACCTA
804895 AAGTG-ATAATATGATATATGTT
1 AAGTGAAT-ATATGATATATGTT
*
804917 AAGTGAATATGTGATATATGT
1 AAGTGAATATATGATATATGT
804938 CATGTCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.40
Consensus pattern (22 bp):
AAGTGAATATATGATATATGTT
Found at i:805989 original size:18 final size:20
Alignment explanation
Indices: 805949--805991 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
805939 TAGAATAGCA
*
805949 TGAATTCGATGCTATGAAGT
1 TGAATTCGATGCTATGAAAT
805969 TGAATTC-ATGCT-TGAAAT
1 TGAATTCGATGCTATGAAAT
805987 TGAAT
1 TGAAT
805992 GGAAATCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 5 0.23
20 7 0.32
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (20 bp):
TGAATTCGATGCTATGAAAT
Found at i:807975 original size:14 final size:14
Alignment explanation
Indices: 807958--807991 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
807948 CAGTGAGTAG
807958 TTATCAGTTATC-AA
1 TTATCAGTT-TCAAA
807972 TTATCAGTTTCAAA
1 TTATCAGTTTCAAA
807986 TTATCA
1 TTATCA
807992 ACACCGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (14 bp):
TTATCAGTTTCAAA
Found at i:812819 original size:15 final size:13
Alignment explanation
Indices: 812777--812827 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 13
812767 ATTTTAAAAT
*
812777 TTAATTTGTATATT
1 TTAATTT-TATATA
812791 TTAATTTTATTATA
1 TTAATTTTA-TATA
812805 TTGAATTTATATATA
1 TT-AATTT-TATATA
812820 TTAATTTT
1 TTAATTTT
812828 GTTTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 3 0.09
14 17 0.52
15 11 0.33
16 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (13 bp):
TTAATTTTATATA
Found at i:821453 original size:39 final size:37
Alignment explanation
Indices: 821404--821483 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 37
821394 AAAAAGACTT
* *
821404 AAAATAAAGGA-CGAATTAAAGAAATAAAAAGATTATGA
1 AAAATAAAGGATCAAATTAAA-AAATAAAAA-ATTATCA
* *
821442 AAAATTAAAGGATTAAATTGAAAAATAAAAAATTATCA
1 AAAA-TAAAGGATCAAATTAAAAAATAAAAAATTATCA
821480 AAAA
1 AAAA
821484 GAGAAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 14 0.39
39 16 0.44
40 6 0.17
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.21
Consensus pattern (37 bp):
AAAATAAAGGATCAAATTAAAAAATAAAAAATTATCA
Found at i:821669 original size:153 final size:154
Alignment explanation
Indices: 821402--821684 Score: 396
Period size: 153 Copynumber: 1.8 Consensus size: 154
821392 TAAAAAAGAC
*
821402 TTAAAATAAAGGACGAATTAAAGAAATAAAAAGATTATGAAAAATTAAAGGATTAAATTGAAAAA
1 TTAAAATAAAGGACGAATTAAAGAAATAAAAAGATTATGAAAAATTAAAGGACTAAATTGAAAAA
* *
821467 TAAAAAATTATCAAAAAGAGAAATTGAAAGTACACATGTATTCTACTATGGTTTAGGAGCATGTG
66 TAAAAAATTATCAAAAAGAGAAATTGAAAGTAAAAATGTATTCTACTATGGTTTAGGAGCATGTG
821532 AATCAAATTTGATAAAAATCGGGT
131 AATCAAATTTGATAAAAATCGGGT
* * * ** *
821556 TTAAAATAAATGATGAATTGAAGAAATAAGGAGATTA-GAAAAATTGAAGGACTAAATTGAAAAA
1 TTAAAATAAAGGACGAATTAAAGAAATAAAAAGATTATGAAAAATTAAAGGACTAAATTGAAAAA
* *
821620 TAAAAATTTGTTATCAAAAAGAGGAATT-AAAGTTAAAAATGTA-T-T-CTATGGTTTAGGAGCA
66 TAAAAA---ATTATCAAAAAGAGAAATTGAAAG-TAAAAATGTATTCTACTATGGTTTAGGAGCA
821681 TGTG
127 TGTG
821685 GTTCGAATTT
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
153 51 0.45
154 33 0.29
155 5 0.04
156 25 0.22
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.28
Consensus pattern (154 bp):
TTAAAATAAAGGACGAATTAAAGAAATAAAAAGATTATGAAAAATTAAAGGACTAAATTGAAAAA
TAAAAAATTATCAAAAAGAGAAATTGAAAGTAAAAATGTATTCTACTATGGTTTAGGAGCATGTG
AATCAAATTTGATAAAAATCGGGT
Found at i:825297 original size:18 final size:19
Alignment explanation
Indices: 825276--825321 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
825266 CAGGTTGTAC
*
825276 ATAATTTTGAC-TTTATTT
1 ATAATTTTGACATCTATTT
*
825294 ATAATTTTTTACATCTATTT
1 ATAA-TTTTGACATCTATTT
825314 ATAATTTT
1 ATAATTTT
825322 AAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (19 bp):
ATAATTTTGACATCTATTT
Found at i:825330 original size:18 final size:19
Alignment explanation
Indices: 825288--825331 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
825278 AATTTTGACT
* *
825288 TTATTTATAATTTTTTACA
1 TTATTTATAATTTTTAAAA
825307 TCTATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
825326 TTATTT
1 TTATTT
825332 TACATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:827415 original size:23 final size:22
Alignment explanation
Indices: 827357--827429 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 22
827347 CACCAAAGCT
*
827357 CACATAATTTG-CACCGAAGTG-C
1 CACATAGTTTGTC-CCGAAG-GAC
827379 CACATA-TTTGTCCCGAAGGAC
1 CACATAGTTTGTCCCGAAGGAC
827400 CACATAGTTTTGTCCCGAAGGAC
1 CACATAG-TTTGTCCCGAAGGAC
827423 CACATAG
1 CACATAG
827430 AACCCTCGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.02
21 17 0.36
22 7 0.15
23 22 0.47
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (22 bp):
CACATAGTTTGTCCCGAAGGAC
Found at i:830020 original size:22 final size:22
Alignment explanation
Indices: 829977--830020 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
829967 AAATTTACAT
*
829977 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
829999 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
830021 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:831889 original size:25 final size:27
Alignment explanation
Indices: 831837--831889 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
831827 GGCACTCACT
* *
831837 CGGCTGAGAGGCTGGAACGTCAAGCGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
*
831864 CGGCTG-GA-GCTGGAAGGCCAAACGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
831889 C
1 C
831890 TGAGCTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.23, C:0.25, G:0.43, T:0.09
Consensus pattern (27 bp):
CGGCTGAGAGGCTGGAACGCCAAACGG
Found at i:832022 original size:25 final size:25
Alignment explanation
Indices: 831987--832088 Score: 186
Period size: 25 Copynumber: 4.1 Consensus size: 25
831977 CGGCTGGAAC
831987 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
832012 TTTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
832037 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
832062 ATTTAGGGTTTGAAACCCTAATATG
1 ATTTAGGGTTTGAAACCCTAATCTG
832087 AT
1 AT
832089 GGGTTGATTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (25 bp):
ATTTAGGGTTTGAAACCCTAATCTG
Found at i:832138 original size:20 final size:21
Alignment explanation
Indices: 832099--832139 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
832089 GGGTTGATTG
832099 TTGGGCTCCGGGATTGGGCCTA
1 TTGGGCTCCGGGA-TGGGCCTA
*
832121 TTGGGCTTCGGG-TGGGCCT
1 TTGGGCTCCGGGATGGGCCT
832140 TGTTGTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.05, C:0.22, G:0.44, T:0.29
Consensus pattern (21 bp):
TTGGGCTCCGGGATGGGCCTA
Found at i:832203 original size:3 final size:3
Alignment explanation
Indices: 832178--832228 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
832168 ATGTAAAATG
* *
832178 TAA TAT TAA TAA T-A TAG TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
832223 AAA TAA
1 TAA TAA
832229 CGATAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:832574 original size:40 final size:41
Alignment explanation
Indices: 832428--832972 Score: 283
Period size: 43 Copynumber: 12.5 Consensus size: 41
832418 CGTCTAAAGG
* *
832428 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCTATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATC-TGG--ATCT---GGGGA
* * * * * ** *
832475 TAACACGGTTCCTACGTGATGAGGACAGCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCTGGGGA
832518 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGATCTGGGGA
* * *
832558 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCT---GGGGA
* * * * * * ** *
832604 TAACATGGTTCCTACGTGATGAGGACAGCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCTGGGGA
832647 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGATCTGGGG-A
* * *
832687 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCT---GGGGA
* * * * * ** *
832733 TAACACGGTTCCTACGTGATGAGGACAGCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCTGGGGA
832776 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGATCTGGGG-A
* * *
832816 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCT---GGGGA
* * * * ** *
832862 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAAGA-GATCTGG--ATCTGGGGA
* * *
832905 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCT---GGGGA
* *
832951 TAACACGGTTCCTACGTGATGA
1 TGACACGGCTCCTACGTGATGA
832973 GGACGGCTGG
Statistics
Matches: 374, Mismatches: 97, Indels: 55
0.71 0.18 0.10
Matches are distributed among these distances:
39 4 0.01
40 99 0.26
42 1 0.00
43 120 0.32
46 120 0.32
47 30 0.08
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (41 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGATCTGGGGA
Found at i:832621 original size:129 final size:129
Alignment explanation
Indices: 832428--832936 Score: 939
Period size: 129 Copynumber: 3.9 Consensus size: 129
832418 CGTCTAAAGG
* *
832428 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCTATCTAAAGGTGATAACACGGTTCCTACGTG
1 TGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
832493 ATGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCTGGGG-
65 ATGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGGA
832557 A
129 A
*
832558 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
832623 TGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
66 TGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
832687 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
832752 TGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
66 TGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
832816 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
* * *
832881 TGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGTTCTGG
66 TGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGG
832937 CCATCTAAAG
Statistics
Matches: 371, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
128 4 0.01
129 339 0.91
130 28 0.08
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (129 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
TGAGGACAGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
Found at i:832678 original size:89 final size:89
Alignment explanation
Indices: 832558--832988 Score: 413
Period size: 89 Copynumber: 4.9 Consensus size: 89
832548 GGTCTGGGGA
*
832558 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
832623 TGAGGACAGCTGGTTATCTATGGT
66 TGAGGACAGCTGGTTATCTATGGT
* * * * * *
832647 TGACACGGCTCCTACGTGATGAAGAGATCTGG---TC----GGGGAATGACACGGCTCATACGTG
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG-ATAACACGGTTCCTACGTG
* *** ** *
832705 ATGAAGAGTTCTGGCCATCTAAAGGT
65 ATGAGGACAGCTGGTTATCT-ATGGT
* * * * *** ** * * *
832731 GATAACACGGTTCCTACGTGATGAGGACAGCTGGTTATCT-ATGGT--TGACACGGCTCCTACGT
1 --TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGT
* * * ** *
832793 GATGAAGAGATCTGG---TC-GGGGAA
64 GATGAGGACAGCTGGTTATCTATGG-T
832816 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
*
832881 TGAGGACGGCTGGTTATCTATGGT
66 TGAGGACAGCTGGTTATCTATGGT
832905 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
*
832970 TGAGGACGGCTGGTTATCT
66 TGAGGACAGCTGGTTATCT
832989 CTAGGGATAA
Statistics
Matches: 280, Mismatches: 44, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
82 3 0.01
83 58 0.21
84 10 0.04
86 57 0.20
89 148 0.53
90 2 0.01
92 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (89 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
TGAGGACAGCTGGTTATCTATGGT
Found at i:833246 original size:60 final size:62
Alignment explanation
Indices: 833173--833293 Score: 160
Period size: 60 Copynumber: 2.0 Consensus size: 62
833163 CCAAAGCAAC
*
833173 TGTCTCGAAAGAGACAAAA-TTCGTTTCAAAG-GAAACA-ACCCAAAGATTTTTTCACAAAAT
1 TGTCTCGAAAGAGACAAAACTTCGTTTCAAAGTAAAACAGACCCAAAGATTTTTTC-CAAAAT
* * *
833233 TGTCTC-AAGAGAGACAAAACTTTGTTTCAAAGTAAAATAGACTCAAAGATTTTTTCCAAAA
1 TGTCTCGAA-AGAGACAAAACTTCGTTTCAAAGTAAAACAGACCCAAAGATTTTTTCCAAAA
833294 GAAATTGTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
59 2 0.04
60 16 0.30
61 11 0.21
62 9 0.17
63 15 0.28
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (62 bp):
TGTCTCGAAAGAGACAAAACTTCGTTTCAAAGTAAAACAGACCCAAAGATTTTTTCCAAAAT
Found at i:833325 original size:65 final size:62
Alignment explanation
Indices: 833126--833343 Score: 194
Period size: 65 Copynumber: 3.4 Consensus size: 62
833116 AGATATTTGC
* * * *
833126 TTTGTTTC-AAGTGAAATAAACTCAAAGATAAGTTTTTCCAAAGCAACTGTCTCGAAAGAGACAA
1 TTTGTTTCAAAG-GAAACAGACTCAAAGAT---TTTTTCCAAAGAAATTGTCTC-AAAGAGACAA
833190 AA
61 AA
* * *
833192 TTCGTTTCAAAGGAAACA-ACCCAAAGATTTTTT-CACA-AAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTCCAAAGAAATTGTCTCAA-AGAGACAAAA
* * ** *
833252 CTTTGTTTCAAAGTAAAATAGACTCAAAGATTTTTTCCAAAAGAAATTGTCTTTAAGAGATAAAA
1 -TTTGTTTCAAAG-GAAACAGACTCAAAGATTTTTTCC-AAAGAAATTGTCTCAAAGAGACAAAA
833317 TTTTGTTTCAGAA-GAAACAGACTCAAA
1 -TTTGTTTCA-AAGGAAACAGACTCAAA
833344 TGATGGATCT
Statistics
Matches: 126, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
59 2 0.02
60 18 0.14
61 14 0.11
62 9 0.07
63 14 0.11
64 13 0.10
65 29 0.23
66 24 0.19
67 3 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.29
Consensus pattern (62 bp):
TTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTCCAAAGAAATTGTCTCAAAGAGACAAAA
Found at i:833647 original size:29 final size:29
Alignment explanation
Indices: 833610--834081 Score: 209
Period size: 29 Copynumber: 15.8 Consensus size: 29
833600 TTAAGAGAGA
*
833610 CAAA-ATTTTGTTTCAAAAGAAACAAACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* *
833638 C-AAGATTTTTGTTTCAAAAGAAACTATCTT
1 CAAAGATTTTT-TTTCAAAAGAAACAAAC-T
* * *
833668 AAGAGAGAAAAAAATTTTGTTTCCAAAGAAACAAACT
1 CA-A-AG------ATTTTTTTTCAAAAGAAACAAACT
*
833705 CAAAGA---TTTTTCAAAAGAAAC-GACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* * *
833730 CAAAGATATTTATTCAAAAGGAACAAACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* * *
833759 CCAAGA-TTTTATTCAAAAGGAACAAACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* ***
833787 CAAAGATTTTTTTTCAAGAGAAACTGTCT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* * * *
833816 CAAGAGAGACAAAACTTTGTTTT-AAAATAAATAGACT
1 C-A-A-AG-----A-TTTTTTTTCAAAAGAAACAAACT
* * *
833853 CAAAGATATTTATTCAAAAGGAACAAACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* * *
833882 CCAAGATTTTTATTCAAAAGGAACAAACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* ***
833911 CAAAGA-TTTTTTTCAAGAGAAACTGTCT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* * * *
833939 CAAGAGAGACAAAACTTTGTTTT-AAAATAAATAGACT
1 C-A-A-AG-----A-TTTTTTTTCAAAAGAAACAAACT
833976 CAAAGA---TTTTTCAAAAGAAAC-AACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* * *
834001 CAAAGATATTTATTCAAAAGGAACAAACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
* * *
834030 CCAAGATTTTTATTCAAAAGGAACAAACT
1 CAAAGATTTTTTTTCAAAAGAAACAAACT
*
834059 CAAAGA-TTTTTTTCAAGAGAAAC
1 CAAAGATTTTTTTTCAAAAGAAAC
834082 TGTCTCAAGA
Statistics
Matches: 338, Mismatches: 64, Indels: 84
0.70 0.13 0.17
Matches are distributed among these distances:
25 22 0.07
26 20 0.06
27 2 0.01
28 94 0.28
29 122 0.36
30 3 0.01
31 3 0.01
32 3 0.01
33 2 0.01
34 4 0.01
35 4 0.01
36 4 0.01
37 23 0.07
38 27 0.08
39 5 0.01
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (29 bp):
CAAAGATTTTTTTTCAAAAGAAACAAACT
Found at i:833769 original size:28 final size:28
Alignment explanation
Indices: 833692--834081 Score: 216
Period size: 29 Copynumber: 13.3 Consensus size: 28
833682 TTTTGTTTCC
833692 AAAGAAACAAACTCAAAGA-TTT-TTCA
1 AAAGAAACAAACTCAAAGATTTTATTCA
*
833718 AAAGAAAC-GACTCAAAGATATTTATTCA
1 AAAGAAACAAACTCAAAGAT-TTTATTCA
* *
833746 AAAGGAACAAACTCCAAGATTTTATTCA
1 AAAGAAACAAACTCAAAGATTTTATTCA
* *
833774 AAAGGAACAAACTCAAAGATTTTTTTTCA
1 AAAGAAACAAACTCAAAGA-TTTTATTCA
* *** ** *
833803 AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTA
1 AAAGAAACAAACTC-A-A-AG-----A-TTTTATTCA
* * *
833840 AAATAAATAGACTCAAAGATATTTATTCA
1 AAAGAAACAAACTCAAAGAT-TTTATTCA
* *
833869 AAAGGAACAAACTCCAAGATTTTTATTCA
1 AAAGAAACAAACTCAAAGA-TTTTATTCA
* *
833898 AAAGGAACAAACTCAAAGATTTTTTTCA
1 AAAGAAACAAACTCAAAGATTTTATTCA
* *** ** *
833926 AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTA
1 AAAGAAACAAACTC-A-A-AG-----A-TTTTATTCA
* * *
833963 AAATAAATAGACTCAAAGA-TTT-TTCA
1 AAAGAAACAAACTCAAAGATTTTATTCA
833989 AAAGAAAC-AACTCAAAGATATTTATTCA
1 AAAGAAACAAACTCAAAGAT-TTTATTCA
* *
834017 AAAGGAACAAACTCCAAGATTTTTATTCA
1 AAAGAAACAAACTCAAAGA-TTTTATTCA
* *
834046 AAAGGAACAAACTCAAAGATTTTTTTCA
1 AAAGAAACAAACTCAAAGATTTTATTCA
*
834074 AGAGAAAC
1 AAAGAAAC
834082 TGTCTCAAGA
Statistics
Matches: 283, Mismatches: 52, Indels: 56
0.72 0.13 0.14
Matches are distributed among these distances:
25 18 0.06
26 17 0.06
27 8 0.03
28 80 0.28
29 109 0.39
30 4 0.01
31 3 0.01
32 2 0.01
34 4 0.01
35 2 0.01
36 3 0.01
37 33 0.12
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (28 bp):
AAAGAAACAAACTCAAAGATTTTATTCA
Found at i:833865 original size:123 final size:123
Alignment explanation
Indices: 833726--834046 Score: 553
Period size: 123 Copynumber: 2.6 Consensus size: 123
833716 CAAAAGAAAC
833726 GACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTATTCAAAAGGAACAAACTCAAA
1 GACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTATTCAAAAGGAACAAACTCAAA
833791 GATTTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATA
66 GATTTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATA
833849 GACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAAACTCAA
1 GACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGA-TTTTATTCAAAAGGAACAAACTCAA
833914 AGA-TTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATA
65 AGATTTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATA
* * *
833972 GACTCAAAG--ATTT-TTCAAAAGAAAC-AACTCAAAGATATTTATTCAAAAGGAACAAACTCCA
1 GACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGAT-TTTATTCAAAAGGAACAAACTCAA
*
834033 AGATTTTTATTCAA
65 AGATTTTTTTTCAA
834047 AAGGAACAAA
Statistics
Matches: 191, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
118 1 0.01
119 35 0.18
120 20 0.10
121 4 0.02
123 103 0.54
124 28 0.15
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (123 bp):
GACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTATTCAAAAGGAACAAACTCAAA
GATTTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAAATAAATA
Found at i:834402 original size:36 final size:36
Alignment explanation
Indices: 834318--834421 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 36
834308 GAGAAAATGA
* * *
834318 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
* ** *
834352 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
*
834388 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
834422 ACGATCTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.18
36 28 0.49
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
Found at i:834449 original size:36 final size:36
Alignment explanation
Indices: 834319--834437 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
834309 AGAAAATGAT
* * * *
834319 GTCTCAAGCGAGACGAAATTTG-CTTTA-AG-ATAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* **
834352 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 -GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
834389 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
834424 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
834438 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 19 0.28
35 11 0.16
36 37 0.54
37 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:834568 original size:105 final size:105
Alignment explanation
Indices: 834432--834621 Score: 292
Period size: 105 Copynumber: 1.8 Consensus size: 105
834422 ACGATCTCAA
* * *
834432 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAATGTCTCA
1 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAATATCTCA
834497 AACGAGACGCAATTTGTTTTGAAAGAAACAACAATCTAAG
66 AACGAGACGCAATTTGTTTTGAAAGAAACAACAATCTAAG
* * * *
834537 GTGAGATTAATTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATATCTC
1 GTGAGATCAACTTTG-TTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAATATCTC
*
834601 AAGCGAGACGCAATTTGTTTT
65 AAACGAGACGCAATTTGTTTT
834622 AAAATTCTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
105 71 0.93
106 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (105 bp):
GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAATATCTCA
AACGAGACGCAATTTGTTTTGAAAGAAACAACAATCTAAG
Found at i:835084 original size:4 final size:4
Alignment explanation
Indices: 835075--835137 Score: 112
Period size: 4 Copynumber: 16.2 Consensus size: 4
835065 TTTATGTATC
835075 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
835121 ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT A
835138 CTTTTCTCGA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
4 55 0.96
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:836320 original size:18 final size:18
Alignment explanation
Indices: 836297--836331 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
836287 TTCTTTGTCC
836297 TCTTTG-TTCTTTGCTTTT
1 TCTTTGATT-TTTGCTTTT
836315 TCTTTGATTTTTGCTTT
1 TCTTTGATTTTTGCTTT
836332 AATTCTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.03, C:0.14, G:0.11, T:0.71
Consensus pattern (18 bp):
TCTTTGATTTTTGCTTTT
Found at i:841007 original size:22 final size:22
Alignment explanation
Indices: 840964--841007 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
840954 AAATTTACAT
*
840964 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
840986 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
841008 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:842875 original size:25 final size:27
Alignment explanation
Indices: 842823--842875 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
842813 GGCACTCACT
* *
842823 CGGCTGAGAGGCTGGAACGTCAAGCGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
*
842850 CGGCTG-GA-GCTGGAAGGCCAAACGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
842875 C
1 C
842876 TGAGCTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.23, C:0.25, G:0.43, T:0.09
Consensus pattern (27 bp):
CGGCTGAGAGGCTGGAACGCCAAACGG
Found at i:843008 original size:25 final size:25
Alignment explanation
Indices: 842973--843074 Score: 186
Period size: 25 Copynumber: 4.1 Consensus size: 25
842963 CGGCTGGAAC
842973 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
842998 TTTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
843023 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
843048 ATTTAGGGTTTGAAACCCTAATATG
1 ATTTAGGGTTTGAAACCCTAATCTG
843073 AT
1 AT
843075 GGGTTGATTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (25 bp):
ATTTAGGGTTTGAAACCCTAATCTG
Found at i:843124 original size:20 final size:21
Alignment explanation
Indices: 843085--843125 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
843075 GGGTTGATTG
843085 TTGGGCTCCGGGATTGGGCCTA
1 TTGGGCTCCGGGA-TGGGCCTA
*
843107 TTGGGCTTCGGG-TGGGCCT
1 TTGGGCTCCGGGATGGGCCT
843126 TGTTGTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.05, C:0.22, G:0.44, T:0.29
Consensus pattern (21 bp):
TTGGGCTCCGGGATGGGCCTA
Found at i:843189 original size:3 final size:3
Alignment explanation
Indices: 843164--843214 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
843154 ATGTAAAATG
* *
843164 TAA TAT TAA TAA T-A TAG TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
843209 AAA TAA
1 TAA TAA
843215 CGATAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:847920 original size:3 final size:3
Alignment explanation
Indices: 847912--847950 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
847902 TCCGGGTTTT
* *
847912 TTA TTA TTA TCA TTAA TAA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT
847951 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:848230 original size:22 final size:22
Alignment explanation
Indices: 848202--848251 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
848192 ATCATCAACT
*
848202 CAGCCGTTTGGCCTTCCAGTTC
1 CAGCCGTTTGGCCTTCCAGCTC
*
848224 CAGCCGTTTGGCTTTCCAGCTC
1 CAGCCGTTTGGCCTTCCAGCTC
848246 CAGCCG
1 CAGCCG
848252 CCAACCTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.38, G:0.24, T:0.28
Consensus pattern (22 bp):
CAGCCGTTTGGCCTTCCAGCTC
Found at i:849614 original size:18 final size:18
Alignment explanation
Indices: 849571--849614 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
849561 TATGTATAAT
849571 TTATTTTTACTTATGTTA
1 TTATTTTTACTTATGTTA
*
849589 TTGTTTTTACTTAT-TTA
1 TTATTTTTACTTATGTTA
849606 TTATATTTT
1 TTAT-TTTT
849615 CTTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
TTATTTTTACTTATGTTA
Found at i:862602 original size:141 final size:138
Alignment explanation
Indices: 862383--862694 Score: 387
Period size: 141 Copynumber: 2.2 Consensus size: 138
862373 CAACATCAAC
**
862383 TGACCAGATATCCTCGA-CACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCAC
1 TGACCAGACCTCCTC-ATCACGTAGGAGCAGTGTCAACATTAGGATAACCAGCCGTCCTCATCAC
* * **
862446 GTAGGAACCAAGTTATCACCCTTCCTAAAGATGGCCAGAATTCTTCATCATGTATGAACCATGTC
65 GTAGGAACCAAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACATATGAACCATGTC
862511 ATCTACCCTTAGA
130 A--T--CCTTAGA
* * * *
862524 TGACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCATTACG
1 TGACCAGACCTCCTCATCACGTAGGAGCAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
* * * * *
862588 TAGGAACCTAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCATATGAGCCGTGTCA
66 TAGGAACCAAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACATATGAACCATGTCA
862653 TCCTTAGA
131 TCCTTAGA
* * * *
862661 CGACCAGACCTCTTCATCATGTATGAGCAGTGTC
1 TGACCAGACCTCCTCATCACGTAGGAGCAGTGTC
862695 GTCCCCAACA
Statistics
Matches: 149, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
137 36 0.24
139 1 0.01
140 1 0.01
141 100 0.67
142 11 0.07
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (138 bp):
TGACCAGACCTCCTCATCACGTAGGAGCAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
TAGGAACCAAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACATATGAACCATGTCA
TCCTTAGA
Found at i:863159 original size:22 final size:22
Alignment explanation
Indices: 863131--863180 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
863121 ATCATCAACT
*
863131 CAGCCGTTTGGCCTTCCAGTTC
1 CAGCCGTTTGGCCTTCCAGCTC
*
863153 CAGCCGTTTGGCTTTCCAGCTC
1 CAGCCGTTTGGCCTTCCAGCTC
863175 CAGCCG
1 CAGCCG
863181 CCAACCTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.38, G:0.24, T:0.28
Consensus pattern (22 bp):
CAGCCGTTTGGCCTTCCAGCTC
Found at i:864544 original size:18 final size:18
Alignment explanation
Indices: 864501--864544 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
864491 TATGTATAAT
864501 TTATTTTTACTTATGTTA
1 TTATTTTTACTTATGTTA
*
864519 TTGTTTTTACTTAT-TTA
1 TTATTTTTACTTATGTTA
864536 TTATATTTT
1 TTAT-TTTT
864545 CTTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
TTATTTTTACTTATGTTA
Found at i:864595 original size:2 final size:2
Alignment explanation
Indices: 864583--864612 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
864573 ATATTAGGAA
*
864583 AT AT TT 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
864613 TGGTTAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:867839 original size:130 final size:130
Alignment explanation
Indices: 867699--867946 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
867689 ATTATTTATA
*
867699 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
867764 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
867829 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
867894 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
867947 GAAGAAATTA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:868435 original size:15 final size:17
Alignment explanation
Indices: 868415--868446 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
868405 ATTTCTTATT
868415 AAAATA-AAAT-ATTCA
1 AAAATATAAATGATTCA
868430 AAAATATAAATGATTCA
1 AAAATATAAATGATTCA
868447 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATATAAATGATTCA
Found at i:868593 original size:21 final size:21
Alignment explanation
Indices: 868569--868611 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
868559 TATTACCTTA
868569 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
868590 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
868611 A
1 A
868612 TGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:868629 original size:35 final size:35
Alignment explanation
Indices: 868580--868665 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
868570 ATTGAAGTAT
** * * *
868580 TTTAGAATTTAATTGAAGTATTTTAGAATTTATGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
868615 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
868650 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
868666 TGACTGTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:870899 original size:143 final size:141
Alignment explanation
Indices: 870739--871025 Score: 540
Period size: 143 Copynumber: 2.0 Consensus size: 141
870729 ATCAAAACAA
870739 TCAAATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTTGTAGGTGGAAAACATGAAACAC
1 TCAAATAATTTTGTGTGTAAATGAAATTATTAAATTAATA-TTGTAGGTGGAAAACATGAAACAC
870804 TATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATATATCATTTTTATAAAAG
65 TATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAG--TATATCATTTTTATAAAAG
870868 TGTCCATACTTATT
128 TGTCCATACTTATT
870882 TCAAATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
1 TCAAATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
870947 ATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATATCATTTTTATAAAAGTGT
66 ATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATATCATTTTTATAAAAGTGT
871012 CCATACTTATT
131 CCATACTTATT
871023 TCA
1 TCA
871026 CTGTGGAAAA
Statistics
Matches: 143, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
141 36 0.25
142 28 0.20
143 79 0.55
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (141 bp):
TCAAATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
ATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATATCATTTTTATAAAAGTGT
CCATACTTATT
Found at i:871311 original size:20 final size:19
Alignment explanation
Indices: 871288--871334 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
871278 CGATATACCA
871288 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
871308 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
871328 GGTAAAA
1 GGTAAAA
871335 CGTTACCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:871488 original size:20 final size:19
Alignment explanation
Indices: 871460--871515 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
871450 GATCCACAAC
*
871460 GATATAACAGGTAAAAATAT
1 GATAAAACAGGTAAAAA-AT
* *
871480 GATAAAACATGTATCAAAAT
1 GATAAAACAGGTA-AAAAAT
*
871500 GATAAAACCGGTAAAA
1 GATAAAACAGGTAAAA
871516 TGATACTGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.21
Consensus pattern (19 bp):
GATAAAACAGGTAAAAAAT
Found at i:873767 original size:21 final size:21
Alignment explanation
Indices: 873743--873786 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
873733 AAGACAATCA
873743 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
873764 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
873785 AG
1 AG
873787 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:873861 original size:32 final size:33
Alignment explanation
Indices: 873820--873884 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
873810 AAATAGATGG
*
873820 AGTGGTGAAAGAAGTAGAGGT-TTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
873852 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
873885 TATTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:875698 original size:19 final size:19
Alignment explanation
Indices: 875674--875722 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
875664 AATATAGGGT
875674 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
875693 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
875712 TATTTTTGTAT
1 TAATTTTGTAT
875723 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:876250 original size:199 final size:199
Alignment explanation
Indices: 875841--876807 Score: 1750
Period size: 199 Copynumber: 4.9 Consensus size: 199
875831 CAATATGGCC
* *
875841 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAATATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
875906 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
875971 G-A-A--TCTAAATAA--TGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCATAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
876030 TGGAA
195 TGGAA
876035 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
876100 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACTGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
876165 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
876230 GGAA
196 GGAA
876234 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
876299 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
876364 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
876429 GGAA
196 GGAA
*
876433 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACT
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
* *
876498 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGATACAAATATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
876563 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
876628 GGAA
196 GGAA
* *
876632 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
* **
876697 CAAAGGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTAGATTGAGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA-TGAGA
*
876762 GAATATGTCTAAAAAATGTGTCGACACT-TTTTAGTTTGTGTCGATA
130 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA
876808 CTAATTTAAA
Statistics
Matches: 749, Mismatches: 17, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
193 67 0.09
194 61 0.08
195 1 0.00
197 9 0.01
199 579 0.77
200 32 0.04
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAA
Found at i:878292 original size:12 final size:12
Alignment explanation
Indices: 878275--878357 Score: 94
Period size: 12 Copynumber: 6.7 Consensus size: 12
878265 GGTCGCAGAA
*
878275 GATGAAGCTGAC
1 GATGAAGATGAC
878287 GATGAAGATGAC
1 GATGAAGATGAC
*
878299 GATGATGATGAC
1 GATGAAGATGAC
*
878311 GATGAAGCTGAC
1 GATGAAGATGAC
878323 GATGAAGATGATGAC
1 GATG-A-A-GATGAC
* *
878338 GATGATGATGAT
1 GATGAAGATGAC
878350 GATGAAGA
1 GATGAAGA
878358 AGATGATGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
12 48 0.80
13 1 0.02
14 2 0.03
15 9 0.15
ACGTcount: A:0.37, C:0.08, G:0.34, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:878296 original size:6 final size:6
Alignment explanation
Indices: 878272--878363 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
878262 AGCGGTCGCA
* * * * * *
878272 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * * *
878320 GACGAT GAAGAT GATGAC GATGAT GATGAT GATGAA GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
878364 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.39, C:0.08, G:0.34, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:878307 original size:3 final size:3
Alignment explanation
Indices: 878287--878367 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
878277 TGAAGCTGAC
* * * * * * *
878287 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
878335 GAC GAT GAT GAT GAT GAT GAA GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
878368 CCAAACAAGT
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.22
Consensus pattern (3 bp):
GAT
Found at i:878322 original size:36 final size:39
Alignment explanation
Indices: 878275--878356 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 39
878265 GGTCGCAGAA
878275 GATGAAGCTGACGATG-A-A-GATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
*
878311 GATGAAGCTGACGATGAAGATGATGACGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
878350 GATGAAG
1 GATGAAG
878357 AAGATGATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
36 16 0.38
37 1 0.02
38 1 0.02
39 24 0.57
ACGTcount: A:0.37, C:0.09, G:0.34, T:0.21
Consensus pattern (39 bp):
GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
Found at i:879592 original size:16 final size:16
Alignment explanation
Indices: 879560--879593 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
879550 TATCCACAAC
* *
879560 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
879576 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
879592 AA
1 AA
879594 TGTAATAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:879930 original size:23 final size:21
Alignment explanation
Indices: 879886--879930 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
879876 ATTACATAAC
*
879886 TTTTAAAAAAGTATCGATCTT
1 TTTTAAAAAAGTATCGAACTT
*
879907 TTTTATAAAAAGTATGGACACTT
1 TTTTA-AAAAAGTATCGA-ACTT
879930 T
1 T
879931 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (21 bp):
TTTTAAAAAAGTATCGAACTT
Found at i:879979 original size:23 final size:23
Alignment explanation
Indices: 879948--880011 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
879938 ATAGGTAAAA
*
879948 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCACTT
* *
879971 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCACTT
879994 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
880012 TGGTTATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:880707 original size:182 final size:183
Alignment explanation
Indices: 880400--880891 Score: 914
Period size: 182 Copynumber: 2.7 Consensus size: 183
880390 GCAATGCTAT
* *
880400 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
880465 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
880530 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAA-TTTGTAATATAAC
131 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
880582 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
880647 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAATTGTGTCGATACCATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
*
880712 TTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
*
880765 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCTACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
880830 GTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
880892 GTAATTTTAA
Statistics
Matches: 301, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
182 164 0.54
183 137 0.46
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (183 bp):
CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:883382 original size:25 final size:25
Alignment explanation
Indices: 883348--883412 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
883338 TTATCATTAA
883348 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
**** *
883373 ATTTAGGTATGTTTGTTAACTATAT
1 ATTTAGGTATGTACAATAACTACAT
*
883398 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
883413 TCTTTTGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:883645 original size:25 final size:25
Alignment explanation
Indices: 883611--883661 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
883601 ACAACAAATC
*
883611 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
883636 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
883661 A
1 A
883662 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:884072 original size:18 final size:18
Alignment explanation
Indices: 884051--884087 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
884041 GTAATTGGAG
884051 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
884069 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
884087 T
1 T
884088 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:884095 original size:24 final size:24
Alignment explanation
Indices: 884043--884089 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
884033 TTTCATATGT
* *
884043 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
884067 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
884090 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:884390 original size:39 final size:39
Alignment explanation
Indices: 884343--884429 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
884333 ACCGATGCTC
*
884343 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
884382 ATCCAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
884421 ATCAAAATC
1 ATCAAAATC
884430 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:884856 original size:22 final size:24
Alignment explanation
Indices: 884831--884888 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
884821 AGGTAAAAAT
884831 ATGTAATAGGTAGGCG-CT-TATA
1 ATGTAATAGGTAGGCGTCTATATA
* *
884853 ATGTAATAGGTA-TCGTTTATATA
1 ATGTAATAGGTAGGCGTCTATATA
884876 ATGTAATAGGTAG
1 ATGTAATAGGTAG
884889 TGGTTTGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.06
22 13 0.42
23 16 0.52
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (24 bp):
ATGTAATAGGTAGGCGTCTATATA
Found at i:885051 original size:13 final size:13
Alignment explanation
Indices: 885033--885068 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
885023 ACGTTACGAT
885033 ATTATAAATAAAA
1 ATTATAAATAAAA
*
885046 ATTATAAATAATA
1 ATTATAAATAAAA
*
885059 TTTATAAATA
1 ATTATAAATA
885069 TCAAAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTATAAATAAAA
Found at i:894145 original size:25 final size:25
Alignment explanation
Indices: 894111--894186 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
894101 TCAGATAATC
894111 ATAACACTTGTATCTATTTATACGT
1 ATAACACTTGTATCTATTTATACGT
894136 ATAACACTTGTATCTATTTATACGT
1 ATAACACTTGTATCTATTTATACGT
894161 ATAACACTTGTATCTATTTTATACGT
1 ATAACACTTGTATCTA-TTTATACGT
894187 CTATATCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 41 0.82
26 9 0.18
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (25 bp):
ATAACACTTGTATCTATTTATACGT
Found at i:894598 original size:33 final size:35
Alignment explanation
Indices: 894552--894631 Score: 110
Period size: 33 Copynumber: 2.3 Consensus size: 35
894542 GATTACTAAA
*
894552 CCCGTCCCTGTCCCCGTTTAACATAAAC-G-TTTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTC
**
894585 CCCGTCCCCGTCCCCGTTTAGTATAAACGGTTTTTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACGG-TTTTC
894621 CCCGTCCCCGT
1 CCCGTCCCCGT
894632 TTAATTCGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.61
34 1 0.02
36 15 0.37
ACGTcount: A:0.14, C:0.41, G:0.15, T:0.30
Consensus pattern (35 bp):
CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTC
Found at i:900141 original size:256 final size:257
Alignment explanation
Indices: 899686--900199 Score: 994
Period size: 256 Copynumber: 2.0 Consensus size: 257
899676 ATAAATCTGG
*
899686 ACATATTTGAGGCCAGGTTCCAGTTATAGGAGATGCTTAAGATAATATAAAAAGCTGAAAAATGA
1 ACATATTTGAGGCCAGGTTCCAGTTATAGGAGATGCTTAAGATAACATAAAAAGCTGAAAAATGA
899751 TTAGCTATTTATAAGATAAAAACAAGATTAAAAAACGTCATTTGACCAAAATCAGTATCAAATTC
66 TTAGCTATTTATAAGATAAAAACAAGATTAAAAAACGTCATTTGACCAAAATCAGTATCAAATTC
*
899816 TGATTTAATTTTCGCAAAAATCACGGATTAATTTCTATAATTAATCTACTACAGCTGGATGAACC
131 TGATTTAATTTTCGCAAAAATCACGGATTAATTTCTATAATTAATCTACTACAACTGGATGAACC
899881 TGGCCTCAAATCTGTCCAAATTTATTCATAAAATATAGATGTTACAATAGCTA-TCAGTGGC
196 TGGCCTCAAATCTGTCCAAATTTATTCATAAAATATAGATGTTACAATAGCTATTCAGTGGC
899942 ACATATTTGAGGCCAGGTTCCAGTTATAGGAGATGCTTAAGATAACATAAAAAGCTGAAAAATGA
1 ACATATTTGAGGCCAGGTTCCAGTTATAGGAGATGCTTAAGATAACATAAAAAGCTGAAAAATGA
900007 TTAGCTATTTATAAGATAAAAACAAGATTAAAAAACGTCATTTGACCAAAATCAGTATCAAATTC
66 TTAGCTATTTATAAGATAAAAACAAGATTAAAAAACGTCATTTGACCAAAATCAGTATCAAATTC
*
900072 TGATTTAATTTTCGTAAAAATCACGGATTAATTTCTATAATTAATCTACTACAACTGGATGAACC
131 TGATTTAATTTTCGCAAAAATCACGGATTAATTTCTATAATTAATCTACTACAACTGGATGAACC
900137 TGGCCTCAAATCTGTCCAAATTTATTCATAAAATATAGATGTTACAATAGCTATTCAGTGGC
196 TGGCCTCAAATCTGTCCAAATTTATTCATAAAATATAGATGTTACAATAGCTATTCAGTGGC
900199 A
1 A
900200 GATAAATGGC
Statistics
Matches: 254, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
256 245 0.96
257 9 0.04
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (257 bp):
ACATATTTGAGGCCAGGTTCCAGTTATAGGAGATGCTTAAGATAACATAAAAAGCTGAAAAATGA
TTAGCTATTTATAAGATAAAAACAAGATTAAAAAACGTCATTTGACCAAAATCAGTATCAAATTC
TGATTTAATTTTCGCAAAAATCACGGATTAATTTCTATAATTAATCTACTACAACTGGATGAACC
TGGCCTCAAATCTGTCCAAATTTATTCATAAAATATAGATGTTACAATAGCTATTCAGTGGC
Found at i:908621 original size:50 final size:50
Alignment explanation
Indices: 908561--908668 Score: 207
Period size: 50 Copynumber: 2.2 Consensus size: 50
908551 CAGTTGTTGG
*
908561 GAAATAAACGAGAACTAGTAATTTCTCTATAACCAGATTAGTGAGAATGC
1 GAAATAAACGAGAACTAGTAATTTCTCTATAACCAGATTAATGAGAATGC
908611 GAAATAAACGAGAACTAGTAATTTCTCTATAACCAGATTAATGAGAATGC
1 GAAATAAACGAGAACTAGTAATTTCTCTATAACCAGATTAATGAGAATGC
908661 GAAATAAA
1 GAAATAAA
908669 AGTGGAAAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (50 bp):
GAAATAAACGAGAACTAGTAATTTCTCTATAACCAGATTAATGAGAATGC
Found at i:908642 original size:25 final size:25
Alignment explanation
Indices: 908564--908642 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
908554 TTGTTGGGAA
908564 ATAAACGAGAACTAGTAATTTCTCT
1 ATAAACGAGAACTAGTAATTTCTCT
* * * * ***
908589 AT-AACCAG-ATTAGTGAGAATGCGAA
1 ATAAACGAGAACTAGT-A-ATTTCTCT
908614 ATAAACGAGAACTAGTAATTTCTCT
1 ATAAACGAGAACTAGTAATTTCTCT
908639 ATAA
1 ATAA
908643 CCAGATTAAT
Statistics
Matches: 36, Mismatches: 14, Indels: 8
0.62 0.24 0.14
Matches are distributed among these distances:
23 5 0.14
24 6 0.17
25 14 0.39
26 6 0.17
27 5 0.14
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (25 bp):
ATAAACGAGAACTAGTAATTTCTCT
Found at i:919421 original size:2 final size:2
Alignment explanation
Indices: 919414--919438 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
919404 GGTTTATGAA
919414 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
919439 GCTGTGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:920202 original size:2 final size:2
Alignment explanation
Indices: 920191--920224 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
920181 ATACTTTGCA
920191 AT AT -T 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 AT AT AT A
920225 ACATGAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:924074 original size:99 final size:99
Alignment explanation
Indices: 923903--924102 Score: 400
Period size: 99 Copynumber: 2.0 Consensus size: 99
923893 AATTTTTGCC
923903 AATATTACCCTTTCGGTTAAACTTGTTGCTTATTAAAAAAAAAGGAAAATTACTTCAAATCATTT
1 AATATTACCCTTTCGGTTAAACTTGTTGCTTATTAAAAAAAAAGGAAAATTACTTCAAATCATTT
923968 AATTATGAGTCTGATAATAAATACATATTCTTTT
66 AATTATGAGTCTGATAATAAATACATATTCTTTT
924002 AATATTACCCTTTCGGTTAAACTTGTTGCTTATTAAAAAAAAAGGAAAATTACTTCAAATCATTT
1 AATATTACCCTTTCGGTTAAACTTGTTGCTTATTAAAAAAAAAGGAAAATTACTTCAAATCATTT
924067 AATTATGAGTCTGATAATAAATACATATTCTTTT
66 AATTATGAGTCTGATAATAAATACATATTCTTTT
924101 AA
1 AA
924103 AATATTATAA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (99 bp):
AATATTACCCTTTCGGTTAAACTTGTTGCTTATTAAAAAAAAAGGAAAATTACTTCAAATCATTT
AATTATGAGTCTGATAATAAATACATATTCTTTT
Found at i:924551 original size:13 final size:13
Alignment explanation
Indices: 924533--924558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
924523 ACATATTTAA
924533 ACAGTCTTCATAT
1 ACAGTCTTCATAT
924546 ACAGTCTTCATAT
1 ACAGTCTTCATAT
924559 GCGCGTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:930911 original size:20 final size:20
Alignment explanation
Indices: 930886--930941 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
930876 ACTTCGACTA
930886 TCGCATTGCGATTTACATA-T
1 TCGCATTGCGATTTACA-AGT
* *
930906 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGAT-TTACAAGT
930927 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
930942 TTCCAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAGT
Found at i:931031 original size:99 final size:99
Alignment explanation
Indices: 930916--931114 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
930906 TCGCATTGCG
930916 ATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAAATTGCAACGACGG
1 ATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAAATTGCAACGACGG
930981 TATTGCATTTGTTTCTTAAGAATTTTCTCTAAAA
66 TATTGCATTTGTTTCTTAAGAATTTTCTCTAAAA
931015 ATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAAATTGCAACGACGG
1 ATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAAATTGCAACGACGG
931080 TATTGCATTTGTTTCTTAAGAATTTTCTCTAAAA
66 TATTGCATTTGTTTCTTAAGAATTTTCTCTAAAA
931114 A
1 A
931115 GATAGTATTC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (99 bp):
ATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAAATTGCAACGACGG
TATTGCATTTGTTTCTTAAGAATTTTCTCTAAAA
Found at i:938027 original size:4 final size:4
Alignment explanation
Indices: 938012--938043 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
938002 CATGTAACAA
938012 ATAC ACTAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATA
938044 ACATGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:938460 original size:20 final size:20
Alignment explanation
Indices: 938412--938508 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
938402 CACTGAATAT
938412 TTGTCCCGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
938431 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
938450 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* *
938469 -TATCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
*
938488 TTGTCCCGAAGTACCACTGA
1 TTGTCCCGAAGGACCACTGA
938508 T
1 T
938509 AATCCCTCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 31 0.48
19 2 0.03
20 32 0.49
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:938460 original size:38 final size:38
Alignment explanation
Indices: 938412--938514 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
938402 CACTGAATAT
* *
938412 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATATCCCGAAGGACCACTGA
* *
938450 TTGTTCCGAAGAACCACTATATCCCGAAGGACCACTGT
1 TTGTCCCGAAGAACCACTATATCCCGAAGGACCACTGA
*
938488 TTGTCCCGAAGTACCACTGATAATCCC
1 TTGTCCCGAAGAACCACT-AT-ATCCC
938515 TCGACTCTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 50 0.88
39 2 0.04
40 5 0.09
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATATCCCGAAGGACCACTGA
Found at i:938514 original size:20 final size:19
Alignment explanation
Indices: 938413--938508 Score: 115
Period size: 18 Copynumber: 5.1 Consensus size: 19
938403 ACTGAATATT
938413 TGTCCCGAAGGACCACT-A
1 TGTCCCGAAGGACCACTGA
938431 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACTGA
* *
938450 TTGTTCCGAAGAACCACT-A
1 -TGTCCCGAAGGACCACTGA
* *
938469 TATCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCACTG-A
*
938489 TGTCCCGAAGTACCACTGA
1 TGTCCCGAAGGACCACTGA
938508 T
1 T
938509 AATCCCTCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 31 0.48
19 3 0.05
20 31 0.48
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (19 bp):
TGTCCCGAAGGACCACTGA
Found at i:942363 original size:4 final size:4
Alignment explanation
Indices: 942344--942446 Score: 52
Period size: 4 Copynumber: 25.5 Consensus size: 4
942334 ATTGGTTTAA
* * *
942344 TATT TATT T-TT ATATT TATT TATT TATAAC TATAT AATT TA-C TATT
1 TATT TATT TATT -TATT TATT TATT TAT--T TAT-T TATT TATT TATT
* * * * * *
942390 TATT TATA TATT TA-G TATG TATT TATA TATT TA-C TATT TATT TATA
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
942436 TAGTT TATT TA
1 TA-TT TATT TA
942447 CTATTTATAT
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
3 8 0.11
4 56 0.75
5 8 0.11
6 3 0.04
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (4 bp):
TATT
Found at i:942402 original size:19 final size:19
Alignment explanation
Indices: 942339--942442 Score: 109
Period size: 19 Copynumber: 5.2 Consensus size: 19
942329 ATAATATTGG
* *
942339 TTTAATATTTATTTTTATA
1 TTTACTATTTATTTATATA
* *
942358 TTTATTTATTTATAACTATATAA
1 TTTA-CTATTTAT--TTATAT-A
942381 TTTACTATTTATTTATATA
1 TTTACTATTTATTTATATA
* *
942400 TTTAGTATGTATTTATATA
1 TTTACTATTTATTTATATA
942419 TTTACTATTTATTTATATA
1 TTTACTATTTATTTATATA
942438 GTTTA
1 -TTTA
942443 TTTACTATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
19 39 0.55
20 16 0.23
22 11 0.15
23 5 0.07
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTACTATTTATTTATATA
Found at i:942453 original size:7 final size:6
Alignment explanation
Indices: 942343--942457 Score: 58
Period size: 6 Copynumber: 17.8 Consensus size: 6
942333 TATTGGTTTA
* *
942343 ATATTT ATTTTT ATATTT ATTTATTT ATAACTAT ATAATTT ACTATTT
1 ATATTT ATATTT ATATTT A--TATTT AT-A-TTT AT-ATTT A-TATTT
* *
942391 AT-TTAT ATATTT AGTATGT AT-TTAT ATATTT ACTATTT AT-TTAT ATAGTT
1 ATATT-T ATATTT A-TATTT ATATT-T ATATTT A-TATTT ATATT-T ATATTT
942441 -TATTT ACTATTT ATATT
1 ATATTT A-TATTT ATATT
942458 CTTTTCTATC
Statistics
Matches: 86, Mismatches: 8, Indels: 30
0.69 0.06 0.24
Matches are distributed among these distances:
5 9 0.10
6 33 0.38
7 31 0.36
8 13 0.15
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:942874 original size:43 final size:41
Alignment explanation
Indices: 942824--942950 Score: 136
Period size: 43 Copynumber: 3.0 Consensus size: 41
942814 TTGTAATTAA
942824 ACTCAACAATATCATTTAACAGAACAATACAAGGTAAAATATT
1 ACTCAACAATATCATTTAACA-AACAATA-AAGGTAAAATATT
* *
942867 ACTCAACAATATCATTTAACAATA-AATATATGT-AAATGA--
1 ACTCAACAATATCATTTAACAA-ACAATAAAGGTAAAAT-ATT
* *
942906 ACTCAACAATATCATTTAACATAACAATATGAGGTATAATATT
1 ACTCAACAATATCATTTAACA-AACAATA-AAGGTAAAATATT
942949 AC
1 AC
942951 ACATTTATAT
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
39 22 0.31
40 9 0.13
41 8 0.11
42 8 0.11
43 24 0.34
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (41 bp):
ACTCAACAATATCATTTAACAAACAATAAAGGTAAAATATT
Found at i:942909 original size:82 final size:82
Alignment explanation
Indices: 942798--942950 Score: 227
Period size: 82 Copynumber: 1.9 Consensus size: 82
942788 TACGAGGTAT
*
942798 ATTTAACAAAAAATAATTGTAATTAAACTCAACAATATCATTTAACAGAACAATACAAGGTAAAA
1 ATTTAACAAAAAATAATTGTAAATAAACTCAACAATATCATTTAACAGAACAATACAAGGTAAAA
942863 TATTACTCAACAATATC
66 TATTACTCAACAATATC
* * * ** *
942880 ATTTAACAATAAAT-ATATGTAAATGAACTCAACAATATCATTTAACATAACAATATGAGGTATA
1 ATTTAACAAAAAATAAT-TGTAAATAAACTCAACAATATCATTTAACAGAACAATACAAGGTAAA
942944 ATATTAC
65 ATATTAC
942951 ACATTTATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 2 0.03
82 61 0.97
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (82 bp):
ATTTAACAAAAAATAATTGTAAATAAACTCAACAATATCATTTAACAGAACAATACAAGGTAAAA
TATTACTCAACAATATC
Found at i:942921 original size:39 final size:36
Alignment explanation
Indices: 942798--942926 Score: 123
Period size: 39 Copynumber: 3.2 Consensus size: 36
942788 TACGAGGTAT
*
942798 ATTTAACAAAAAATAATTGTAATTAAACTCAACAATATC
1 ATTTAAC-AAAAATAA-TGTAAAT-AACTCAACAATATC
*
942837 ATTTAACAGAACAATACAAGGTAAAATATTACTCAACAATATC
1 ATTTAACA-AA-AAT--AATGT-AAATA--ACTCAACAATATC
942880 ATTTAACAATAAATATATGTAAATGAACTCAACAATATC
1 ATTTAACAA-AAATA-ATGTAAAT-AACTCAACAATATC
942919 ATTTAACA
1 ATTTAACA
942927 TAACAATATG
Statistics
Matches: 77, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
38 1 0.01
39 30 0.39
40 8 0.10
41 7 0.09
42 9 0.12
43 22 0.29
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (36 bp):
ATTTAACAAAAATAATGTAAATAACTCAACAATATC
Found at i:956773 original size:11 final size:11
Alignment explanation
Indices: 956759--956792 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
956749 AGTGAAAATG
956759 AAAAAT-AAAA
1 AAAAATAAAAA
956769 AAAAATAAAAA
1 AAAAATAAAAA
956780 AAAAATGAAAAA
1 AAAAAT-AAAAA
956792 A
1 A
956793 TGGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.27
11 10 0.45
12 6 0.27
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:956792 original size:10 final size:10
Alignment explanation
Indices: 956759--956783 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
956749 AGTGAAAATG
956759 AAAAATAAAA
1 AAAAATAAAA
956769 AAAAATAAAA
1 AAAAATAAAA
956779 AAAAA
1 AAAAA
956784 ATGAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:956793 original size:36 final size:35
Alignment explanation
Indices: 956730--956805 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 35
956720 TTGCTTGAAG
* *
956730 AAAAAAAAAAAGAAAAATGAGTGAAAATGAAAAATAA
1 AAAAAAAAAAAAAAAAATGAG-AAAAATGAAAAA-AA
*
956767 AAAAAAATAAAAAAAAAATGA-AAAAATGGAAAAAA
1 AAAAAAA-AAAAAAAAAATGAGAAAAATGAAAAAAA
956802 AAAA
1 AAAA
956806 GAAGGGTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 6 0.17
36 10 0.29
37 7 0.20
38 12 0.34
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (35 bp):
AAAAAAAAAAAAAAAAATGAGAAAAATGAAAAAAA
Found at i:956799 original size:21 final size:19
Alignment explanation
Indices: 956729--956805 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 19
956719 TTTGCTTGAA
956729 GAAAAAA-AAAAAGAAAAAT
1 GAAAAAATAAAAA-AAAAAT
* * *
956748 GAGTGAAAATGAAAAATAAA-
1 GA--AAAAATAAAAAAAAAAT
956768 -AAAAAATAAAAAAAAAAT
1 GAAAAAATAAAAAAAAAAT
956786 GAAAAAATGGAAAAAAAAAA
1 GAAAAAAT--AAAAAAAAAA
956806 GAAGGGTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
17 13 0.29
19 10 0.22
21 18 0.40
22 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (19 bp):
GAAAAAATAAAAAAAAAAT
Found at i:957766 original size:55 final size:55
Alignment explanation
Indices: 957697--958285 Score: 559
Period size: 55 Copynumber: 11.0 Consensus size: 55
957687 AGGTTTCCCA
*
957697 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
957752 ACGATTGTTGAAGATCGTTCGAG--TCATACTCTCTTAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
957805 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
957860 ACGATTGTTGAAAATTGTTCGAGTCTTATACTCTCTGCATAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
957915 ACGACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
957970 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
958025 ACGATTGATGAAGATTCTTCAAGT-TCCATACTCCCT--AGAGAA-AGGGAGC-GA-
1 ACGATTGTTGAAGATTGTTCGAGTCT-CATACTCTCTGAAGA-AATAGGGAGCAGAC
* * * *
958076 ACCCA--GTTGAAGA-TGTTCGAGT-TCCATACTC-CTTAAAGAAAGAAGGAGC-GA-
1 A-CGATTGTTGAAGATTGTTCGAGTCT-CATACTCTC-TGAAGAAATAGGGAGCAGAC
** * *
958127 AC--CCGTTGAAGAGATGTTCGAGT-TCCATACTCCCT-AGAGAAATAGGGA-C-GA-
1 ACGATTGTTGAAGA-TTGTTCGAGTCT-CATACTCTCTGA-AGAAATAGGGAGCAGAC
* *
958178 ACCCATTTGTTGAAGATTGTTCGAGT-T-ATACTCTCTGAAGAAATAGGGGGCAGAC
1 A-CGA-TTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
958233 GCGATCG-TGAAGATTGTTCGAGTC-C-TATCTCTCTGAAG-AATAGGGGGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATA-CTCTCTGAAGAAATAGGGAGCAGAC
958285 A
1 A
958286 AGTTGTGAAG
Statistics
Matches: 463, Mismatches: 45, Indels: 55
0.82 0.08 0.10
Matches are distributed among these distances:
48 1 0.00
49 17 0.04
50 18 0.04
51 18 0.04
52 83 0.18
53 73 0.16
54 17 0.04
55 236 0.51
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:958179 original size:51 final size:50
Alignment explanation
Indices: 958046--958204 Score: 198
Period size: 52 Copynumber: 3.1 Consensus size: 50
958036 AGATTCTTCA
958046 AGTTCCATACTCCCTAGAG-AAAGGGAGCGAACCCAGTTGAAGATGTTCG
1 AGTTCCATACTCCCTAGAGAAAAGGGAGCGAACCCAGTTGAAGATGTTCG
* * *
958095 AGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTGAAGAGATGTTCG
1 AGTTCCATACTCCCTAGAGAAA-AGGGAGCGAACCCAGTTG-A-AGATGTTCG
958147 AGTTCCATACTCCCTAGAGAAATAGGGA-CGAACCCATTTGTTGAAGATTGTTCG
1 AGTTCCATACTCCCTAGAGAAA-AGGGAGCGAACCCA---GTTGAAGA-TGTTCG
958201 AGTT
1 AGTT
958205 ATACTCTCTG
Statistics
Matches: 94, Mismatches: 7, Indels: 13
0.82 0.06 0.11
Matches are distributed among these distances:
49 17 0.18
50 6 0.06
51 20 0.21
52 33 0.35
53 3 0.03
54 11 0.12
55 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (50 bp):
AGTTCCATACTCCCTAGAGAAAAGGGAGCGAACCCAGTTGAAGATGTTCG
Found at i:960352 original size:24 final size:23
Alignment explanation
Indices: 960325--960370 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
960315 ATTACTACTT
*
960325 TATGTATGGTATGTACATTTTTAG
1 TATGTATGGTATGCA-ATTTTTAG
*
960349 TATGTATGTTATGCAATTTTTA
1 TATGTATGGTATGCAATTTTTA
960371 TTTATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.52
Consensus pattern (23 bp):
TATGTATGGTATGCAATTTTTAG
Found at i:970155 original size:137 final size:136
Alignment explanation
Indices: 969875--970155 Score: 350
Period size: 137 Copynumber: 2.1 Consensus size: 136
969865 GATTAAGAAT
**
969875 TTTTTTTTGATGTCTCATATTCAAATACCATGTATATAAGAGTGTATGAGCATTTAGTATCGAAT
1 TTTTTTTTGATGTCTCATATTCAAATACCACATATATAAGAGTGTATGAGCATTTAGTATCGAAT
* * * ** *
969940 GGTTGAACGTCTTTAAATGGATATTACTTTATATTCATCTCTCAGCGATCTCAATGATTAAGAAA
66 GGTTGAACGTCTTTAAATAGATATTACTTTATATTCATCCCTCAGCGATATCAATGAGAAAAAAA
* *
970005 TTATTA
131 CTAATA
* *
970011 TTATTTTTTGATGTCTCATATTCAAATACCACATATGTAAGAGTGTATGAGCGTTTAGTATCGAA
1 TT-TTTTTTGATGTCTCATATTCAAATACCACATATATAAGAGTGTATGAGCATTTAGTATCGAA
* * ***
970076 TGGTTGAACGTCTTTGAATAGATATTAGC-TTATATTCATCCCTCCTTG-GATATTTTTGAGAAA
65 TGGTTGAACGTCTTTAAATAGATATTA-CTTTATATTCATCCCT-C-AGCGATATCAATGAGAAA
*
970139 AAAACTAATG
127 AAAACTAATA
970149 TTTTTTT
1 TTTTTTT
970156 CCTGTACTGT
Statistics
Matches: 123, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
136 2 0.02
137 101 0.82
138 19 0.15
139 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (136 bp):
TTTTTTTTGATGTCTCATATTCAAATACCACATATATAAGAGTGTATGAGCATTTAGTATCGAAT
GGTTGAACGTCTTTAAATAGATATTACTTTATATTCATCCCTCAGCGATATCAATGAGAAAAAAA
CTAATA
Found at i:973968 original size:4 final size:4
Alignment explanation
Indices: 973959--973987 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
973949 ATTTGTTATT
973959 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
973988 CATAAACAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:975866 original size:443 final size:443
Alignment explanation
Indices: 975037--975921 Score: 1752
Period size: 443 Copynumber: 2.0 Consensus size: 443
975027 GGTGCAACTC
975037 CAAAGGATATTACCGCGGAAATGGTATGATATTATCATTCGAATACGAATTCAGACATTTACATT
1 CAAAGGATATTACCGCGGAAATGGTATGATATTATCATTCGAATACGAATTCAGACATTTACATT
*
975102 TGAATTCGAATAACATGATTTGCCTTTGAGGGTTAGGATGTATGGTTTTGATTGATTAAGGAAAT
66 CGAATTCGAATAACATGATTTGCCTTTGAGGGTTAGGATGTATGGTTTTGATTGATTAAGGAAAT
975167 GTTCGATTTTCTAGTTCAACAGAGAAGCTGGGAATGTGGTTGAGGAATGCAAGTTGAGAGTGGTC
131 GTTCGATTTTCTAGTTCAACAGAGAAGCTGGGAATGTGGTTGAGGAATGCAAGTTGAGAGTGGTC
975232 TATGTTTTTTCACCTCAAGATGCAGCTGCACATGATGGGTCTGAAGTAGGGTCTTCAATGAGAGG
196 TATGTTTTTTCACCTCAAGATGCAGCTGCACATGATGGGTCTGAAGTAGGGTCTTCAATGAGAGG
975297 ATCCGTCTCGGACAATGGCCAGGCGAACGCTACTGAGTTCGTTATGGTACCGAAACCGAGATCTT
261 ATCCGTCTCGGACAATGGCCAGGCGAACGCTACTGAGTTCGTTATGGTACCGAAACCGAGATCTT
*
975362 GCTGTGACTATTTTTGTTATTGCCTCTGTTGTTTGCACAATGTTTTTCTGGAACGCTAATAGTTT
326 GCTGTGACTATTTTTGTTATTGCCTCTGTTGTTTGCACAATGTTTTTCTGGAACCCTAATAGTTT
975427 GCATTTGGTGAATGCAGGCTGCAAGAACATTTACAGAAGAAGTTCAAGATAAT
391 GCATTTGGTGAATGCAGGCTGCAAGAACATTTACAGAAGAAGTTCAAGATAAT
975480 CAAAGGATATTACCGCGGAAATGGTATGATATTATCATTCGAATACGAATTCAGACATTTACATT
1 CAAAGGATATTACCGCGGAAATGGTATGATATTATCATTCGAATACGAATTCAGACATTTACATT
975545 CGAATTCGAATAACATGATTTGCCTTTGAGGGTTAGGATGTATGGTTTTGATTGATTAAGGAAAT
66 CGAATTCGAATAACATGATTTGCCTTTGAGGGTTAGGATGTATGGTTTTGATTGATTAAGGAAAT
975610 GTTCGATTTTCTAGTTCAACAGAGAAGCTGGGAATGTGGTTGAGGAATGCAAGTTGAGAGTGGTC
131 GTTCGATTTTCTAGTTCAACAGAGAAGCTGGGAATGTGGTTGAGGAATGCAAGTTGAGAGTGGTC
975675 TATGTTTTTTCACCTCAAGATGCAGCTGCACATGATGGGTCTGAAGTAGGGTCTTCAATGAGAGG
196 TATGTTTTTTCACCTCAAGATGCAGCTGCACATGATGGGTCTGAAGTAGGGTCTTCAATGAGAGG
975740 ATCCGTCTCGGACAATGGCCAGGCGAACGCTACTGAGTTCGTTATGGTACCGAAACCGAGATCTT
261 ATCCGTCTCGGACAATGGCCAGGCGAACGCTACTGAGTTCGTTATGGTACCGAAACCGAGATCTT
975805 GCTGTGACTATTTTTGTTATTGCCTCTGTTGTTTGCACAATGTTTTTCTGGAACCCTAATAGTTT
326 GCTGTGACTATTTTTGTTATTGCCTCTGTTGTTTGCACAATGTTTTTCTGGAACCCTAATAGTTT
975870 GCATTTGGTGAATGCAGGCTGCAAGAACATTTACAGAAGAAGTTCAAGATAA
391 GCATTTGGTGAATGCAGGCTGCAAGAACATTTACAGAAGAAGTTCAAGATAA
975922 ATCTCCTGAG
Statistics
Matches: 440, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
443 440 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (443 bp):
CAAAGGATATTACCGCGGAAATGGTATGATATTATCATTCGAATACGAATTCAGACATTTACATT
CGAATTCGAATAACATGATTTGCCTTTGAGGGTTAGGATGTATGGTTTTGATTGATTAAGGAAAT
GTTCGATTTTCTAGTTCAACAGAGAAGCTGGGAATGTGGTTGAGGAATGCAAGTTGAGAGTGGTC
TATGTTTTTTCACCTCAAGATGCAGCTGCACATGATGGGTCTGAAGTAGGGTCTTCAATGAGAGG
ATCCGTCTCGGACAATGGCCAGGCGAACGCTACTGAGTTCGTTATGGTACCGAAACCGAGATCTT
GCTGTGACTATTTTTGTTATTGCCTCTGTTGTTTGCACAATGTTTTTCTGGAACCCTAATAGTTT
GCATTTGGTGAATGCAGGCTGCAAGAACATTTACAGAAGAAGTTCAAGATAAT
Found at i:984236 original size:55 final size:55
Alignment explanation
Indices: 984176--984285 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
984166 AACAGTCATC
984176 ACTTGTATAACCTAGAGAACGACTAATGCACCAACAGAATACATTTGTTTTACTA
1 ACTTGTATAACCTAGAGAACGACTAATGCACCAACAGAATACATTTGTTTTACTA
984231 ACTTGTATAACCTAGAGAACGACTAATGCACCAACAGAATACATTTGTTTTACTA
1 ACTTGTATAACCTAGAGAACGACTAATGCACCAACAGAATACATTTGTTTTACTA
984286 TTGAACAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (55 bp):
ACTTGTATAACCTAGAGAACGACTAATGCACCAACAGAATACATTTGTTTTACTA
Found at i:988535 original size:22 final size:23
Alignment explanation
Indices: 988490--988537 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
988480 TTATATTTTT
*
988490 AATTTTGTAAAAAAAATTATATA
1 AATTTTATAAAAAAAATTATATA
*
988513 AATTTTATAAAGAAAA-TATATA
1 AATTTTATAAAAAAAATTATATA
988535 AAT
1 AAT
988538 ATTTTTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AATTTTATAAAAAAAATTATATA
Found at i:988720 original size:20 final size:20
Alignment explanation
Indices: 988695--988751 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
988685 TCTTATTCCC
988695 TGGTAATTTTACATTCCCAT
1 TGGTAATTTTACATTCCCAT
*
988715 TGGTAATCTTACATTCCCAT
1 TGGTAATTTTACATTCCCAT
** *
988735 TAATAATTTTATATTCC
1 TGGTAATTTTACATTCC
988752 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (20 bp):
TGGTAATTTTACATTCCCAT
Found at i:997159 original size:7 final size:7
Alignment explanation
Indices: 997147--997172 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
997137 TTTCTCAACC
997147 ATTGAGG
1 ATTGAGG
997154 ATTGAGG
1 ATTGAGG
997161 ATTGAGG
1 ATTGAGG
997168 ATTGA
1 ATTGA
997173 AGGTGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (7 bp):
ATTGAGG
Found at i:998225 original size:2 final size:2
Alignment explanation
Indices: 998220--998244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
998210 AGGAGGTGTG
998220 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
998245 CGAAACCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1001876 original size:16 final size:17
Alignment explanation
Indices: 1001852--1001895 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1001842 AAAATTGGTT
*
1001852 TTCAAGTCTTCAATAAC
1 TTCAAGTCTTCAACAAC
*
1001869 TT-AAGTCTACAACAAC
1 TTCAAGTCTTCAACAAC
1001885 TTCAA-TCTTCA
1 TTCAAGTCTTCA
1001896 CGTAGGCCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (17 bp):
TTCAAGTCTTCAACAAC
Found at i:1004412 original size:197 final size:198
Alignment explanation
Indices: 1004018--1004413 Score: 785
Period size: 197 Copynumber: 2.0 Consensus size: 198
1004008 CAATCGAGCA
1004018 ATAGACTAGTTCGCTATGGCATTCACACAAACAGCGATGAAGCAATATAAACATTCACAAACTGA
1 ATAGACTAGTTCGCTATGGCATTCACACAAACAGCGATGAAGCAATATAAACATTCACAAACTGA
1004083 CTTCCGAAACTGATAGAAACCCACATAGTATTTCCAAACTTTGAAACAAATATCATAAGCAAACC
66 CTTCCGAAACTGATAGAAACCCACATAGTATTTCCAAACTTTGAAACAAATATCATAAGCAAACC
1004148 AAATCTTAAGCACGAAACAACAATCACTAGGAAACAGGAATATACTCACTTCTAGAGGAGAAATA
131 AAATCTTAAGCACGAAACAACAATCACTAGGAAACAGGAATATACTCACTTCTAGAGGAGAAATA
1004213 ATC
196 ATC
1004216 ATAGACTAGTTCGCTATGGCATTCACACAAACAGCGATGAAGCAATATAAACATTCACAAACTGA
1 ATAGACTAGTTCGCTATGGCATTCACACAAACAGCGATGAAGCAATATAAACATTCACAAACTGA
1004281 CTTCCGAAACTGATAGAAACCCACATAGTATTT-CAAACTTTGAAACAAATATCATAAGCAAACC
66 CTTCCGAAACTGATAGAAACCCACATAGTATTTCCAAACTTTGAAACAAATATCATAAGCAAACC
1004345 AAATCTTAAGCACGAAACAACAATCACTAGGAAACAGGAATATACTCACTTCTAGAGGAGAAATA
131 AAATCTTAAGCACGAAACAACAATCACTAGGAAACAGGAATATACTCACTTCTAGAGGAGAAATA
1004410 ATC
196 ATC
1004413 A
1 A
1004414 ATCTCACCAA
Statistics
Matches: 198, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
197 100 0.51
198 98 0.49
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.21
Consensus pattern (198 bp):
ATAGACTAGTTCGCTATGGCATTCACACAAACAGCGATGAAGCAATATAAACATTCACAAACTGA
CTTCCGAAACTGATAGAAACCCACATAGTATTTCCAAACTTTGAAACAAATATCATAAGCAAACC
AAATCTTAAGCACGAAACAACAATCACTAGGAAACAGGAATATACTCACTTCTAGAGGAGAAATA
ATC
Found at i:1007179 original size:64 final size:63
Alignment explanation
Indices: 1007092--1007232 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
1007082 TCTTTAACAT
* * *
1007092 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
1007155 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
1007219 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1007233 ATTGAATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Done.