Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_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: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 20
Found at i:851970 original size:43 final size:43
Alignment explanation
Indices: 851923--852073 Score: 144
Period size: 43 Copynumber: 3.5 Consensus size: 43
851913 TTTTTACAAA
* * * *
851923 AAACGCCGCAATAGGTATTGATATTTAGTGGCATTTGTGTGAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCTCAC
* * * *
851966 AAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTT-TTTATAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCT-CAC
* * * *
852009 AAATGTCGCAATAGGT-TATGATGTTTAGCAGCGTTTGTCTCAC
1 AAACGCCGCAATAGGTAT-TGATATTTAGCGGCGTTTGTCTCAC
* *
852052 AAACGCCACAGTAGGTATTGAT
1 AAACGCCGCAATAGGTATTGAT
852074 GTTTTGCGAT
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 3 0.03
43 81 0.93
44 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCTCAC
Found at i:852531 original size:21 final size:21
Alignment explanation
Indices: 852507--852567 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
852497 GATATGTTGT
*
852507 TTCTCTCTGTGCTGCTGCTGC
1 TTCTCTCTGTGCTACTGCTGC
* * *
852528 TTCTCTTTGTGTTACCGCTGC
1 TTCTCTCTGTGCTACTGCTGC
* * *
852549 TTCTTTCTCTGCTTCTGCT
1 TTCTCTCTGTGCTACTGCT
852568 ACTGCTCTGG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.02, C:0.31, G:0.18, T:0.49
Consensus pattern (21 bp):
TTCTCTCTGTGCTACTGCTGC
Found at i:861600 original size:40 final size:40
Alignment explanation
Indices: 861542--861621 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
861532 TATTACGATG
*
861542 TTTTTTTATAAACACCGCTAAAGAACATGGATATTACGGC
1 TTTTTTTACAAACACCGCTAAAGAACATGGATATTACGGC
** * *
861582 TTTTTTTACAAATGCCGCTAAAGTACATGGATATTGCGGC
1 TTTTTTTACAAACACCGCTAAAGAACATGGATATTACGGC
861622 ATTTGATCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (40 bp):
TTTTTTTACAAACACCGCTAAAGAACATGGATATTACGGC
Found at i:861647 original size:41 final size:41
Alignment explanation
Indices: 861602--861680 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
861592 AATGCCGCTA
*
861602 AAGTACATGGATATTGCGGCATTTGATCACAAACGCCAGAT
1 AAGTACAAGGATATTGCGGCATTTGATCACAAACGCCAGAT
* **
861643 AAGTACAAGGCTATTGCGGCATTTTCTCACAAACGCCA
1 AAGTACAAGGATATTGCGGCATTTGATCACAAACGCCA
861681 CTAAATTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
AAGTACAAGGATATTGCGGCATTTGATCACAAACGCCAGAT
Found at i:862989 original size:22 final size:22
Alignment explanation
Indices: 862964--863009 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
862954 ACGTTTTCAG
*
862964 AAACTATTATTTTCCTATTAGA
1 AAACAATTATTTTCCTATTAGA
* *
862986 AAACAATTATTTTTCTATTCGA
1 AAACAATTATTTTCCTATTAGA
863008 AA
1 AA
863010 GCAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (22 bp):
AAACAATTATTTTCCTATTAGA
Found at i:863606 original size:83 final size:83
Alignment explanation
Indices: 863519--863741 Score: 204
Period size: 83 Copynumber: 2.7 Consensus size: 83
863509 GCATAAATGC
* * ** * *
863519 CACTATAAACAACCCTTTTGCGACGTTTGTTTAATAAACGCCGCTAAATTACTTCTCAATAGTAT
1 CACTATAAACAACACTTTTGCG-CGTTTGTATAATAAACGCCGCTAAATTACCACTCAATAGCAG
*
863584 TGTTTGTTGAAGAAA-CGA
65 TGTTTGTTGAAAAAAGCGA
* * * * * * *
863602 CACTATAAATAACACTATCGCGGCGTTTGTATAA-AAACGTCGCTAAATTACCACTCTATTGCGG
1 CACTATAAACAACACTTTTGC-GCGTTTGTATAATAAACGCCGCTAAATTACCACTCAATAGCAG
*
863666 TGTTTGTTGAAAAAAGCGC
65 TGTTTGTTGAAAAAAGCGA
* *
863685 CACTATAAACAACTCTATTATG-GCGTTTG-AGCT-ATAAACGCCGCTAAATTATCACTC
1 CACTATAAACAACACT-TT-TGCGCGTTTGTA--TAATAAACGCCGCTAAATTACCACTC
863742 TATTGCGACG
Statistics
Matches: 112, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
82 37 0.33
83 51 0.46
84 23 0.21
85 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (83 bp):
CACTATAAACAACACTTTTGCGCGTTTGTATAATAAACGCCGCTAAATTACCACTCAATAGCAGT
GTTTGTTGAAAAAAGCGA
Found at i:863733 original size:166 final size:164
Alignment explanation
Indices: 863436--863735 Score: 365
Period size: 165 Copynumber: 1.8 Consensus size: 164
863426 TTATAAAAAT
* * * **
863436 GACACGATAAACAACATATTGCGGCGTTTTCTCACAAACGCCGCTAAATTATTACTCTATTGCGG
1 GACACGATAAACAACATATCGCGGCGTTTTATCAAAAACGCCGCTAAATTACCACTCTATTGCGG
* * * * **
863501 CATTTTTTGCATAAATGCCACTATAAACAACCCTTTTGCGACGTTTGTTTAATAAACGCCGCTAA
66 CATTTGTTGAAAAAACGCCACTATAAACAACCCTTTTGCGACGTTTGGCTAATAAACGCCGCTAA
863566 ATTACTTCTCAATAGTATTGTTTGTTGAAGAAAC
131 ATTACTTCTCAATAGTATTGTTTGTTGAAGAAAC
* * *
863600 GACACTATAAATAACACTATCGCGGCGTTTGTAT-AAAAACGTCGCTAAATTACCACTCTATTGC
1 GACACGATAAACAACA-TATCGCGGCGTTT-TATCAAAAACGCCGCTAAATTACCACTCTATTGC
** *
863664 GGTGTTTGTTGAAAAAAGCGCCACTATAAACAACTCTATTATG-G-CGTTTGAGCT-ATAAACGC
64 GGCATTTGTTGAAAAAA-CGCCACTATAAACAACCCT-TT-TGCGACGTTTG-GCTAATAAACGC
863726 CGCTAAATTA
125 CGCTAAATTA
863736 TCACTCTATT
Statistics
Matches: 113, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
164 14 0.12
165 50 0.44
166 43 0.38
167 4 0.04
168 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (164 bp):
GACACGATAAACAACATATCGCGGCGTTTTATCAAAAACGCCGCTAAATTACCACTCTATTGCGG
CATTTGTTGAAAAAACGCCACTATAAACAACCCTTTTGCGACGTTTGGCTAATAAACGCCGCTAA
ATTACTTCTCAATAGTATTGTTTGTTGAAGAAAC
Found at i:865486 original size:14 final size:14
Alignment explanation
Indices: 865467--865495 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
865457 TCGATTATAT
865467 GTTCATTTATGTTC
1 GTTCATTTATGTTC
865481 GTTCATTTATGTTC
1 GTTCATTTATGTTC
865495 G
1 G
865496 AACAGAGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:874396 original size:27 final size:27
Alignment explanation
Indices: 874363--874419 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
874353 GAGATTTTTT
874363 TTTCTTACCCGATGATAATGTAATTTC
1 TTTCTTACCCGATGATAATGTAATTTC
*
874390 TTTCTTATCCGATGATAATGTAATTTC
1 TTTCTTACCCGATGATAATGTAATTTC
874417 TTT
1 TTT
874420 TATCTAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.49
Consensus pattern (27 bp):
TTTCTTACCCGATGATAATGTAATTTC
Found at i:875134 original size:20 final size:20
Alignment explanation
Indices: 875109--875150 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
875099 ATAGTTTTAT
*
875109 ACCTTCCAGGATGTTCTAGA
1 ACCTTCCAGAATGTTCTAGA
*
875129 ACCTTCCATAATGTTCTAGA
1 ACCTTCCAGAATGTTCTAGA
875149 AC
1 AC
875151 TTCTATGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (20 bp):
ACCTTCCAGAATGTTCTAGA
Found at i:875948 original size:41 final size:39
Alignment explanation
Indices: 875868--875948 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 39
875858 TTGATAATCT
* *
875868 TAATAATAATATACTATTTTTTTTATAATTATAATATTA
1 TAATAATAATATACTATTTTTTTAATAATAATAATATTA
875907 TAATATATAATAATACT-TTTATTTTAATATATAATAA-ATTA
1 TAATA-ATAAT-ATACTATTT-TTTTAATA-ATAATAATATTA
875948 T
1 T
875949 TGATAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
39 5 0.14
40 8 0.22
41 17 0.47
42 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (39 bp):
TAATAATAATATACTATTTTTTTAATAATAATAATATTA
Found at i:876188 original size:3 final size:3
Alignment explanation
Indices: 876180--876219 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
876170 ATTTTTATAA
876180 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
876220 TCATCATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:876197 original size:14 final size:14
Alignment explanation
Indices: 876180--876219 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
876170 ATTTTTATAA
876180 ATTATTATTATTAT
1 ATTATTATTATTAT
876194 ATTATTATTATTAT
1 ATTATTATTATTAT
*
876208 TTTATTATTATT
1 ATTATTATTATT
876220 TCATCATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:876202 original size:17 final size:17
Alignment explanation
Indices: 876180--876219 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
876170 ATTTTTATAA
876180 ATTATTATTATTATATT
1 ATTATTATTATTATATT
*
876197 ATTATTATTATTTTATT
1 ATTATTATTATTATATT
876214 ATTATT
1 ATTATT
876220 TCATCATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATTATTATTATATT
Found at i:876220 original size:11 final size:12
Alignment explanation
Indices: 876180--876219 Score: 66
Period size: 11 Copynumber: 3.5 Consensus size: 12
876170 ATTTTTATAA
876180 ATTATTATTATT
1 ATTATTATTATT
876192 A-TATTATTATT
1 ATTATTATTATT
876203 ATTATT-TTATT
1 ATTATTATTATT
876214 ATTATT
1 ATTATT
876220 TCATCATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 22 0.81
12 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:879831 original size:18 final size:18
Alignment explanation
Indices: 879808--879864 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
879798 TATATTTTCC
879808 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
*
879826 AACAATTGATATCCTTTTGTT
1 AACAATTGGTAT-C-TTT-TT
879847 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
879865 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 4 0.12
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (18 bp):
AACAATTGGTATCTTTTT
Found at i:879850 original size:21 final size:20
Alignment explanation
Indices: 879808--879864 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
879798 TATATTTTCC
879808 AACAATTGGTAT-C-TTTTT
1 AACAATTGGTATCCTTTTTT
*
879826 AACAATTGATATCCTTTTGTT
1 AACAATTGGTATCCTTTT-TT
879847 AACAATTGGTAT-CTTTTT
1 AACAATTGGTATCCTTTTT
879865 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.32
19 2 0.06
20 8 0.24
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (20 bp):
AACAATTGGTATCCTTTTTT
Found at i:880521 original size:3 final size:3
Alignment explanation
Indices: 880507--880541 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
880497 CCTGCAAACA
* *
880507 AAC AAC ACC AAC AAC AAC AAC AAC AAC AAA AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
880542 ACAGAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:881208 original size:18 final size:18
Alignment explanation
Indices: 881185--881237 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
881175 CGTTTTAAAA
881185 ATTAATTATTATTATATG
1 ATTAATTATTATTATATG
881203 ATTAATTATTATTAGTAT-
1 ATTAATTATTATTA-TATG
* *
881221 TTTAA-AATTATTATATG
1 ATTAATTATTATTATATG
881238 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 18 0.58
19 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
ATTAATTATTATTATATG
Found at i:881316 original size:18 final size:20
Alignment explanation
Indices: 881280--881317 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
881270 AGGATTAATA
881280 TATTATTTAGTAATCATTTAT
1 TATTATTTAGTAA-CATTTAT
881301 TATTATTT-GTAA-ATTTA
1 TATTATTTAGTAACATTTA
881318 AATATAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTATTTAGTAACATTTAT
Found at i:882336 original size:46 final size:50
Alignment explanation
Indices: 882261--882352 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 50
882251 TTATTTATTA
* *
882261 TTATTCTCAGAATAAATACATGCGAACTAGAAATCATGTGGTTAGGTTTG
1 TTATTCTCAGAATAAATACATGCGAACTAGAAAACATGAGGTTAGGTTTG
*
882311 TTATTCT-A-AATAAA-GCATG-GAACTAGAAAACATGAGGTTAGG
1 TTATTCTCAGAATAAATACATGCGAACTAGAAAACATGAGGTTAGG
882353 ATATGTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 21 0.54
47 4 0.10
48 6 0.15
49 1 0.03
50 7 0.18
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (50 bp):
TTATTCTCAGAATAAATACATGCGAACTAGAAAACATGAGGTTAGGTTTG
Found at i:887978 original size:19 final size:20
Alignment explanation
Indices: 887956--887993 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
887946 AAAGGTCATA
* *
887956 CATTT-CATTAATACATTTG
1 CATTTGCATAAATAAATTTG
887975 CATTTGCATAAATAAATTT
1 CATTTGCATAAATAAATTT
887994 TTCATAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
CATTTGCATAAATAAATTTG
Found at i:888886 original size:17 final size:18
Alignment explanation
Indices: 888856--888889 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
888846 GATATGTATA
888856 TATATAATAATATTATTT
1 TATATAATAATATTATTT
*
888874 TATA-AATATTATTATT
1 TATATAATAATATTATT
888890 ACAAAGCCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAATAATATTATTT
Found at i:889358 original size:3 final size:3
Alignment explanation
Indices: 889350--889384 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
889340 CTTGCAAACA
* *
889350 AAC AAC AAC ACC AAC AAC AAC AAC AAC AAA AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
889385 ATAGAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:889619 original size:18 final size:20
Alignment explanation
Indices: 889583--889620 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
889573 GGATTAATAA
889583 TATTATTTAGTAATCATTTAT
1 TATTATTTAGTAA-CATTTAT
889604 TATTATTT-GTAA-ATTTA
1 TATTATTTAGTAACATTTA
889621 AATATAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTATTTAGTAACATTTAT
Found at i:890325 original size:21 final size:21
Alignment explanation
Indices: 890301--890361 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
890291 TTTGAATTTA
890301 ATGAAGGTGTATTGATACCCT
1 ATGAAGGTGTATTGATACCCT
890322 ATGAAGGTGTATTGATA-CCT
1 ATGAAGGTGTATTGATACCCT
* *
890342 ATGAAGGGGTATCGATACCC
1 ATGAAGGTGTATTGATACCC
890362 CCTGTTATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (21 bp):
ATGAAGGTGTATTGATACCCT
Found at i:890344 original size:20 final size:20
Alignment explanation
Indices: 890301--890360 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
890291 TTTGAATTTA
890301 ATGAAGGTGTATTGATACCCT
1 ATGAAGGTGTATTGATA-CCT
890322 ATGAAGGTGTATTGATACCT
1 ATGAAGGTGTATTGATACCT
* *
890342 ATGAAGGGGTATCGATACC
1 ATGAAGGTGTATTGATACC
890361 CCCTGTTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (20 bp):
ATGAAGGTGTATTGATACCT
Found at i:903582 original size:24 final size:24
Alignment explanation
Indices: 903549--903596 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
903539 CGATACCTCC
*
903549 TTGAAGGGGAACCGATTCCCCCCT
1 TTGAAAGGGAACCGATTCCCCCCT
*
903573 TTGAAAGGGAATCGATTCCCCCCT
1 TTGAAAGGGAACCGATTCCCCCCT
903597 GTAGGGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (24 bp):
TTGAAAGGGAACCGATTCCCCCCT
Found at i:903617 original size:22 final size:22
Alignment explanation
Indices: 903533--903619 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
903523 TTAGTGCAGA
* *
903533 GGGAATCGATACCTCCTTGAAG
1 GGGAATCGATACCCCCCTGAAG
* * *
903555 GGGAACCGATTCCCCCCTTTGAAA
1 GGGAATCGATACCCCCC--TGAAG
* *
903579 GGGAATCGATTCCCCCCTGTAG
1 GGGAATCGATACCCCCCTGAAG
903601 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
903620 GGGTTCTGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 34 0.63
24 20 0.37
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (22 bp):
GGGAATCGATACCCCCCTGAAG
Found at i:905212 original size:18 final size:18
Alignment explanation
Indices: 905176--905231 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
905166 CTCCAACGAT
*
905176 GAACCAGAACAGT-ACGAG
1 GAACAAGAACAGTCA-GAG
905194 GAACAAGAACGAG-CAGAG
1 GAACAAGAAC-AGTCAGAG
*
905212 GAACAAGCACAGTCAGAG
1 GAACAAGAACAGTCAGAG
905230 GA
1 GA
905232 TCAAATGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 2 0.06
18 28 0.85
19 3 0.09
ACGTcount: A:0.46, C:0.20, G:0.30, T:0.04
Consensus pattern (18 bp):
GAACAAGAACAGTCAGAG
Found at i:911760 original size:2 final size:2
Alignment explanation
Indices: 911753--911793 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
911743 AGCTATACCC
911753 AT AT AT AT AT AT 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 AT AT AT A
911794 CATCAGCAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:912861 original size:21 final size:21
Alignment explanation
Indices: 912837--912882 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
912827 TTCTTGTTTC
* *
912837 TTTCTCTCTCTTTTTCTATTT
1 TTTCTCTCTCTCTATCTATTT
* *
912858 TTTCTTTCTCTCTATCTTTTT
1 TTTCTCTCTCTCTATCTATTT
912879 TTTC
1 TTTC
912883 CGTCCAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTCTCTCTCTCTATCTATTT
Found at i:913716 original size:10 final size:10
Alignment explanation
Indices: 913697--913729 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
913687 TAAAATATAT
913697 TAATAATAAA
1 TAATAATAAA
*
913707 TAATACTAAA
1 TAATAATAAA
913717 TAATAAT-AA
1 TAATAATAAA
913726 TAAT
1 TAAT
913730 TAAAACCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
TAATAATAAA
Found at i:913742 original size:23 final size:23
Alignment explanation
Indices: 913697--913742 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
913687 TAAAATATAT
* *
913697 TAATAATAAATAATACTAAATAA
1 TAATAATAAATAAAACCAAATAA
* *
913720 TAATAATAATTAAAACCAGATAA
1 TAATAATAAATAAAACCAAATAA
913743 AACGGGTGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (23 bp):
TAATAATAAATAAAACCAAATAA
Found at i:915601 original size:29 final size:30
Alignment explanation
Indices: 915567--915656 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 30
915557 ATTTAAACTC
915567 CTTTTATTATTCAAATTTAAATAGATATTA
1 CTTTTATTATTCAAATTTAAATAGATATTA
* * *
915597 -TTTTAAT-TTGAAATATTCAAAGTATATAATTA
1 CTTTTATTATTCAAAT-TT-AAA-TAGAT-ATTA
*
915629 TCTTTTATTATTCAAAGTTAAATAGATA
1 -CTTTTATTATTCAAATTTAAATAGATA
915657 ATAAATACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
28 6 0.13
29 8 0.17
30 3 0.07
31 5 0.11
32 8 0.17
33 3 0.07
34 8 0.17
35 5 0.11
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (30 bp):
CTTTTATTATTCAAATTTAAATAGATATTA
Found at i:915604 original size:21 final size:22
Alignment explanation
Indices: 915571--915611 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
915561 AAACTCCTTT
915571 TATTATTCAAATTT-AAATAGA
1 TATTATTCAAATTTGAAATAGA
**
915592 TATTATTTTAATTTGAAATA
1 TATTATTCAAATTTGAAATA
915612 TTCAAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TATTATTCAAATTTGAAATAGA
Found at i:915612 original size:63 final size:63
Alignment explanation
Indices: 915494--915656 Score: 188
Period size: 63 Copynumber: 2.5 Consensus size: 63
915484 GTTCCAACTA
* *
915494 AATATCTTTTAATATTCAAATTTAAACAGATAATATTATCTTTTAATTTGAAATATCCAAAAG-A
1 AATATCTTTTATTATTCAAATTTAAATAG---ATATTA-CTTTTAATTTGAAATATCC-AAAGTA
*
915558 TTT
61 TAT
*
915561 AA-ACTCCTTTTATTATTCAAATTTAAATAGATATTA-TTTTAATTTGAAATATTCAAAGTATAT
1 AATA-T-CTTTTATTATTCAAATTTAAATAGATATTACTTTTAATTTGAAATATCCAAAGTATAT
*
915624 AATTATCTTTTATTATTCAAAGTTAAATAGATA
1 AA-TATCTTTTATTATTCAAATTTAAATAGATA
915657 ATAAATACTT
Statistics
Matches: 86, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
62 4 0.05
63 48 0.56
64 1 0.01
65 7 0.08
66 1 0.01
67 3 0.03
68 22 0.26
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (63 bp):
AATATCTTTTATTATTCAAATTTAAATAGATATTACTTTTAATTTGAAATATCCAAAGTATAT
Found at i:916529 original size:15 final size:15
Alignment explanation
Indices: 916509--916544 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
916499 TCTATGGTAT
*
916509 TATGTCGACGATGCA
1 TATGTCGACGACGCA
916524 TATGTCGACGACGCA
1 TATGTCGACGACGCA
916539 TATGTC
1 TATGTC
916545 TTGACTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (15 bp):
TATGTCGACGACGCA
Found at i:919204 original size:21 final size:22
Alignment explanation
Indices: 919171--919211 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
919161 TAAATTCTTT
919171 TATTATTCAAATTT-AAATAGA
1 TATTATTCAAATTTGAAATAGA
**
919192 TATTATTTTAATTTGAAATA
1 TATTATTCAAATTTGAAATA
919212 TTCAAAGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TATTATTCAAATTTGAAATAGA
Found at i:921606 original size:43 final size:43
Alignment explanation
Indices: 921553--921858 Score: 334
Period size: 43 Copynumber: 7.1 Consensus size: 43
921543 TGAGAACAAA
* * * *
921553 AAACGCCGCAATAGGTCAAGATATATAGCGGCGATTTTGGAAT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGATTTTGGAAC
* * *
921596 AAACACCGCAAAAGGTTGAGATCTATAGCGGC-ATTTTTGGAAT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGA-TTTTGGAAC
* * * *
921639 AAACGCCGCAAAAGATCGAGATATATAGCGGTGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGATTTTGGAAC
* *
921682 AAAGGCCGCAAAAGGTTGAGATCTATAGCGGC-ATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGA-TTTTGGAAC
* * *
921725 AAACGCTGCAAAAGGTC-AGATCTATAGCGGTGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGATTTTGGAAC
* * * *
921767 AAACGCCGTAAAAGGTCGAGATCTATAGCAGTGGTTTTGGATA-
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGATTTTGGA-AC
* * *
921810 AAATGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATGC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGATTTTGGA-AC
921853 AAACGC
1 AAACGC
921859 TGCTAGTTAC
Statistics
Matches: 222, Mismatches: 34, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
42 59 0.27
43 162 0.73
44 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGATTTTGGAAC
Found at i:921698 original size:86 final size:85
Alignment explanation
Indices: 921553--921858 Score: 389
Period size: 86 Copynumber: 3.6 Consensus size: 85
921543 TGAGAACAAA
* * * *
921553 AAACGCCGCAATAGGTCAAGATATATAGCGGCGATTTTGGAATAAACACCGCAAAAGGTTGAGAT
1 AAACGCCGCAAAAGGTC-AGATATATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTTGAGAT
921618 CTATAGCGGCATTTTTGGAAT
65 CTATAGCGGCATTTTTGGAAT
* * *
921639 AAACGCCGCAAAAGATCGAGATATATAGCGGTGTTTTTGGAACAAAGGCCGCAAAAGGTTGAGAT
1 AAACGCCGCAAAAGGTC-AGATATATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTTGAGAT
*
921704 CTATAGCGGCATTTTTGGAAC
65 CTATAGCGGCATTTTTGGAAT
* * * * *
921725 AAACGCTGCAAAAGGTCAGATCTATAGCGGTGTTTTTGGAACAAACGCCGTAAAAGGTCGAGATC
1 AAACGCCGCAAAAGGTCAGATATATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTTGAGATC
* ***
921790 TATAGCAGTGGTTTTGG-AT
66 TATAGCGGCATTTTTGGAAT
* * *
921809 AAAATGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATGCAAACGC
1 -AAACGCCGCAAAAGGTCAGATATATAGCGGCGTTTTTGGA-ACAAACGC
921859 TGCTAGTTAC
Statistics
Matches: 194, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 94 0.48
86 99 0.51
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (85 bp):
AAACGCCGCAAAAGGTCAGATATATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTTGAGATC
TATAGCGGCATTTTTGGAAT
Found at i:924669 original size:41 final size:41
Alignment explanation
Indices: 924624--924754 Score: 113
Period size: 41 Copynumber: 3.2 Consensus size: 41
924614 CGATTTGTAT
* * *
924624 AAAAACGTCGCTAAAGTACTATTCTTTTGCGGCGTTTGTTG
1 AAAAACGCCGCTAAAGTACTAATCTATTGCGGCGTTTGTTG
* * * * *
924665 AAAAAACGCCACTATAG-ATTAAACATATTGTGGCGTTTGTAT-
1 -AAAAACGCCGCTAAAGTACTAATC-TATTGCGGCGTTTGT-TG
* * * *
924707 AAAAATGCCGCTAAAGTACTACTCTATTGCGGCATTTATTG
1 AAAAACGCCGCTAAAGTACTAATCTATTGCGGCGTTTGTTG
924748 AAAAACG
1 AAAAACG
924755 TCACTATAGA
Statistics
Matches: 67, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
40 1 0.01
41 35 0.52
42 30 0.45
43 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGTACTAATCTATTGCGGCGTTTGTTG
Found at i:925074 original size:42 final size:43
Alignment explanation
Indices: 924899--925282 Score: 340
Period size: 43 Copynumber: 8.9 Consensus size: 43
924889 TGTAGTACCT
* * * *
924899 ACTTTTTATCTTCATAATTTAGGC-CTTAATTTTTTCAATCTC
1 ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATCTC
* * * *
924941 ACATTTTTACATTTATAATTGATGAC-CTTAAATTTTTCAATCTC
1 AC-TTTTTACCTTTATAATTGA-GGCTCCTAATTTTTTCAATCTC
*
924985 ACTTTGTACCTTTATAATTGA-GCTCCTAATTTTTTTCAATCTC
1 ACTTTTTACCTTTATAATTGAGGCTCCTAA-TTTTTTCAATCTC
* * *
925028 ACTTTCTACCTTTATAATTGA-GCTCCTAATTTTTTCAGTTTC
1 ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATCTC
* * *
925070 ACTTTCTACATTTATAATTGAGAC-CTCTAATTTTTT-AATCTC
1 ACTTTTTACCTTTATAATTGAGGCTC-CTAATTTTTTCAATCTC
* * *
925112 ACTTTTTACCTTTATAATAGATG-TCCTTAATTTTTTTCAATCCC
1 ACTTTTTACCTTTATAATTGAGGCTCC-TAA-TTTTTTCAATCTC
* * * *
925156 ATTTTTTA-CTTGTATAATTTAGGCCCCTAATTTTTTTAATCTC
1 ACTTTTTACCTT-TATAATTGAGGCTCCTAATTTTTTCAATCTC
* * * * *
925199 ACTTTTTACCTTTAAAATTGAGGCCCCT-ATTTTTTTATTCGC
1 ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATCTC
*
925241 ACTTTTTTTA-CTTTATAATTGATG-TCCTTAATTTTTTTCAAT
1 AC--TTTTTACCTTTATAATTGAGGCTCC-TAA-TTTTTTCAAT
925283 AATACCTTTT
Statistics
Matches: 283, Mismatches: 41, Indels: 33
0.79 0.11 0.09
Matches are distributed among these distances:
41 2 0.01
42 80 0.28
43 137 0.48
44 54 0.19
45 10 0.04
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (43 bp):
ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATCTC
Found at i:925211 original size:171 final size:172
Alignment explanation
Indices: 924912--925282 Score: 443
Period size: 171 Copynumber: 2.2 Consensus size: 172
924902 TTTTATCTTC
* * *
924912 ATAATTTAGGCCTTAATTTTTTCAATCTCACATTTTTACATTTATAATTGATGACCTTAAATTTT
1 ATAATTGAGACCTTAATTTTTTCAATCTCACATTTTTACATTTATAATAGATGACCTTAAATTTT
* *
924977 TCAATCTCACTTTGTACCTTTATAATTGAGCTCCTAATTTTTTTCAATCTCACTTTCTACCTTTA
66 TCAATCCCACTTTGTACCTTTATAATTGAGCCCCTAATTTTTTTCAATCTCACTTTCTACCTTTA
* *
925042 TAATTGA-GCTCCTAATTTTTTCAGTTTCACTTTCTACATTT
131 AAATTGAGGCCCCTAATTTTTTCAGTTTCACTTTCTACATTT
* * *
925083 ATAATTGAGACCTCTAATTTTTT-AATCTCAC-TTTTTACCTTTATAATAGATGTCCTTAATTTT
1 ATAATTGAGACCT-TAATTTTTTCAATCTCACATTTTTACATTTATAATAGATGACCTTAA-ATT
* * * *
925146 TTTCAATCCCATTTTTTA-CTTGTATAATTTAGGCCCCTAATTTTTTT-AATCTCACTTTTTACC
64 TTTCAATCCCACTTTGTACCTT-TATAATTGA-GCCCCTAATTTTTTTCAATCTCACTTTCTACC
* * *
925209 TTTAAAATTGAGGCCCCT-ATTTTTTTA-TTCGCACTTTTTTTAC-TTT
127 TTTAAAATTGAGGCCCCTAATTTTTTCAGTT-TCAC--TTTCTACATTT
*
925255 ATAATTGATGTCCTTAATTTTTTTCAAT
1 ATAATTGA-GACCTTAA-TTTTTTCAAT
925283 AATACCTTTT
Statistics
Matches: 171, Mismatches: 18, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
170 30 0.18
171 80 0.47
172 42 0.25
173 16 0.09
174 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.50
Consensus pattern (172 bp):
ATAATTGAGACCTTAATTTTTTCAATCTCACATTTTTACATTTATAATAGATGACCTTAAATTTT
TCAATCCCACTTTGTACCTTTATAATTGAGCCCCTAATTTTTTTCAATCTCACTTTCTACCTTTA
AAATTGAGGCCCCTAATTTTTTCAGTTTCACTTTCTACATTT
Found at i:932586 original size:62 final size:62
Alignment explanation
Indices: 932516--932651 Score: 245
Period size: 62 Copynumber: 2.2 Consensus size: 62
932506 GAAATGAAGA
*
932516 AGGAATTGGGGAAAGAAGAAGTCAAGGGTTGGGGATTGAGGCACGAGATGGGATTGAAAATG
1 AGGAATTGGGGAAAGAAGAAGTCAAGGGTTGGGGATTGAGGCACGAGATGAGATTGAAAATG
932578 AGGAATTGGGGAAAGAAGAAGTCAAGGGTTGGGGATTGAGGCACGAGATGAGATTGAAAATG
1 AGGAATTGGGGAAAGAAGAAGTCAAGGGTTGGGGATTGAGGCACGAGATGAGATTGAAAATG
* *
932640 GGGAATTAGGGA
1 AGGAATTGGGGA
932652 TTGAAGCACG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.36, C:0.04, G:0.42, T:0.18
Consensus pattern (62 bp):
AGGAATTGGGGAAAGAAGAAGTCAAGGGTTGGGGATTGAGGCACGAGATGAGATTGAAAATG
Found at i:936462 original size:30 final size:30
Alignment explanation
Indices: 936426--936644 Score: 377
Period size: 30 Copynumber: 7.3 Consensus size: 30
936416 GAAGGACCTA
936426 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
* *
936456 TCCAGAGATCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
936486 TCCAGAGGTCATAAAGAT-CTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
936515 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
936545 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
936575 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
936605 TTCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
936635 TCCATAGGTC
1 TCCAGAGGTC
936645 CCGAAGAACC
Statistics
Matches: 179, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
29 28 0.16
30 151 0.84
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:936577 original size:89 final size:90
Alignment explanation
Indices: 936423--936644 Score: 401
Period size: 89 Copynumber: 2.5 Consensus size: 90
936413 TCCGAAGGAC
*
936423 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGATCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTATC
936488 CAGAGGTCATAAAGAT-CTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
*
936512 CTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTATC
936577 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* *
936602 CTATTCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTC
936645 CCGAAGAACC
Statistics
Matches: 127, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 79 0.62
90 48 0.38
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (90 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:936661 original size:30 final size:30
Alignment explanation
Indices: 936618--936711 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
936608 AGAGGTCATA
* * *
936618 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
936648 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
936679 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
936710 AA
1 AA
936712 AGACATATGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:941267 original size:30 final size:30
Alignment explanation
Indices: 941015--941256 Score: 448
Period size: 30 Copynumber: 8.1 Consensus size: 30
941005 TCCGAAGGAC
*
941015 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
941045 CTGTCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
941075 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
941105 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
941135 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
941165 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
941195 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
941225 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
941255 CT
1 CT
941257 GTCTATAGGT
Statistics
Matches: 205, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 205 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:943366 original size:18 final size:19
Alignment explanation
Indices: 943343--943379 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
943333 TTCAAAAGAA
943343 GGGATT-GACTAAACTATT
1 GGGATTGGACTAAACTATT
*
943361 GGGATTGGACTACACTATT
1 GGGATTGGACTAAACTATT
943380 CAATACAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (19 bp):
GGGATTGGACTAAACTATT
Found at i:949217 original size:25 final size:25
Alignment explanation
Indices: 949187--949263 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
949177 ATGTATTACG
949187 TATTTATTTTATGTATATTATTATA
1 TATTTATTTTATGTATATTATTATA
* *
949212 TGTTTATTTTACGTATATTATTATA
1 TATTTATTTTATGTATATTATTATA
*
949237 TATATTACTTTAT-TATA-TATTTATA
1 TAT-TTATTTTATGTATATTA-TTATA
949262 TA
1 TA
949264 ATACTACATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
24 2 0.04
25 36 0.80
26 7 0.16
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (25 bp):
TATTTATTTTATGTATATTATTATA
Found at i:955940 original size:9 final size:10
Alignment explanation
Indices: 955928--956029 Score: 73
Period size: 11 Copynumber: 9.5 Consensus size: 10
955918 GAAAATATAT
*
955928 AAAACAAGAA
1 AAAAAAAGAA
955938 AAAAAAAGAA
1 AAAAAAAGAA
* *
955948 AAAAAATATAG
1 AAAAAA-AGAA
*
955959 AGAAAAAGAAA
1 AAAAAAAG-AA
955970 AAAAAAGAGAA
1 AAAAAA-AGAA
955981 GAAAAAGAAGAA
1 -AAAAA-AAGAA
955993 AACAAAAA-ACA
1 AA-AAAAAGA-A
956004 AAAATAAAG-A
1 AAAA-AAAGAA
956014 AAAAAAAGTAA
1 AAAAAAAG-AA
956025 AAAAA
1 AAAAA
956030 TAAAGAAAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 21
0.73 0.07 0.21
Matches are distributed among these distances:
9 4 0.05
10 24 0.32
11 31 0.42
12 14 0.19
13 1 0.01
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.04
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:955953 original size:22 final size:21
Alignment explanation
Indices: 955928--956038 Score: 89
Period size: 21 Copynumber: 5.0 Consensus size: 21
955918 GAAAATATAT
*
955928 AAAACAAGAAAAAAAAAGAAA
1 AAAAAAAGAAAAAAAAAGAAA
* * * *
955949 AAAAATATAGAGAAAAAGAAA
1 AAAAAAAGAAAAAAAAAGAAA
955970 AAAAAAGAGAAGAAAAAGAAGAAA
1 AAAAAA-AGAA-AAAAA-AAGAAA
* *
955994 ACAAAAAACAAAAATAAAGAAA
1 A-AAAAAAGAAAAAAAAAGAAA
*
956016 AAAAAGTAA-AAAAATAAAGAAA
1 AAAAA--AAGAAAAAAAAAGAAA
956038 A
1 A
956039 CCGGTCAAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
21 25 0.34
22 23 0.32
23 10 0.14
24 10 0.14
25 5 0.07
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.05
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAGAAA
Found at i:955957 original size:31 final size:32
Alignment explanation
Indices: 955915--956017 Score: 117
Period size: 31 Copynumber: 3.3 Consensus size: 32
955905 CATAGAGAAA
*
955915 AAAG-AAAATATATAAAACAAGAAAAAAAAAG
1 AAAGAAAAATATAGAAAACAAGAAAAAAAAAG
955946 AAA-AAAAATATAGAGAAA-AAGAAAAAAAAAG
1 AAAGAAAAATATAGA-AAACAAGAAAAAAAAAG
* *
955977 AGAAGAAAAAGA-AGAAAACAA-AAAACAAAAAT
1 A-AAGAAAAATATAGAAAACAAGAAAA-AAAAAG
956009 AAAGAAAAA
1 AAAGAAAAA
956018 AAAGTAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
31 41 0.65
32 16 0.25
33 6 0.10
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.06
Consensus pattern (32 bp):
AAAGAAAAATATAGAAAACAAGAAAAAAAAAG
Found at i:958085 original size:55 final size:55
Alignment explanation
Indices: 958016--958204 Score: 219
Period size: 55 Copynumber: 3.5 Consensus size: 55
958006 TATTAGGAAC
958016 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAAT
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAAT
* * * * *** * *
958071 TAAGTTTGTTTTTCAGAAGTTTCCTGATGA--TTT-AAT-TTTTTTTAAAGAAAC
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAAT
**
958122 TAAGT-TCGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAAT
1 TAAGTCT-GATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAAT
958177 TAAGTCTGATTTTCAG-AGATTTCTTGAC
1 TAAGTCTGATTTTCAGAAG-TTTCTTGAC
958205 AAAATGAATT
Statistics
Matches: 109, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
50 1 0.01
51 35 0.32
52 3 0.03
53 6 0.06
54 5 0.05
55 58 0.53
56 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (55 bp):
TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAAT
Found at i:958337 original size:53 final size:52
Alignment explanation
Indices: 958205--958398 Score: 208
Period size: 52 Copynumber: 3.7 Consensus size: 52
958195 ATTTCTTGAC
* * *
958205 AAAATGAATTTGAAATAAGCTAAGCCTAATTTTTAAGGATTTCACTTGATGTTTT
1 AAAATGAATTTGAAAGAAACTAAGCCTAA-TTTTAAGGGTTT-A-TTGATGTTTT
* *
958260 AAAATGAATTTGAAAAAAACTAAGCCTAATTTTCAAGGGTTTATCGATGTTTT
1 AAAATGAATTTGAAAGAAACTAAGCCTAATTTT-AAGGGTTTATTGATGTTTT
* ** * * * * *
958313 CAAATGAATTTGAAAGAAGTTAAGCTTAATTTTAGGGGTTTCTTAATGTGTT
1 AAAATGAATTTGAAAGAAACTAAGCCTAATTTTAAGGGTTTATTGATGTTTT
* * *
958365 AAAATAAATTTTAAAGAAATTAAGCCTAATTTTA
1 AAAATGAATTTGAAAGAAACTAAGCCTAATTTTA
958399 TGGATTTTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
52 43 0.36
53 37 0.31
54 5 0.04
55 34 0.29
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (52 bp):
AAAATGAATTTGAAAGAAACTAAGCCTAATTTTAAGGGTTTATTGATGTTTT
Found at i:958745 original size:85 final size:85
Alignment explanation
Indices: 958637--958804 Score: 257
Period size: 85 Copynumber: 2.0 Consensus size: 85
958627 AGCAAGATGA
* *
958637 TAAGTCCTTTGGGCCATCCATAAGACATTCGGGCCGGATGTTTTCAACATTTCATTTGT-TCGAT
1 TAAGTCCTTCGGGCCATCCATAAGACATTCGGGCAGGATGTTTTCAACATTTCATTT-TCTCGAT
958701 TCACAACACTTCGAATCAGTT
65 TCACAACACTTCGAATCAGTT
* * * *
958722 TAAGTCCTTCGGGCCATCTATAAGACCTTCGGGGAGGATGTTTTCAACATTTCCTTTTCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACATTCGGGCAGGATGTTTTCAACATTTCATTTTCTCGATT
*
958787 TACAACACTTCGAATCAG
66 CACAACACTTCGAATCAG
958805 CAACGCCCTA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
84 1 0.01
85 74 0.99
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (85 bp):
TAAGTCCTTCGGGCCATCCATAAGACATTCGGGCAGGATGTTTTCAACATTTCATTTTCTCGATT
CACAACACTTCGAATCAGTT
Found at i:958972 original size:41 final size:42
Alignment explanation
Indices: 958866--958972 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
958856 CGAATCAGCC
* * *
958866 TAAGTCATTCGGGCCAT-CAGTAAGTCTTTGGAACATGATGTG
1 TAAGTCATTCGGGCCATCCA-TAAGTCTTTCGAACAAGATGTA
* * *
958908 TAAGTCCTTCGGGCCATCTATAAGTCTTTCGATCAAGATG-A
1 TAAGTCATTCGGGCCATCCATAAGTCTTTCGAACAAGATGTA
*
958949 TAAGTCATTCGGGTCATCCATAAG
1 TAAGTCATTCGGGCCATCCATAAG
958973 ACCTTCAGGC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 21 0.38
42 33 0.60
43 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (42 bp):
TAAGTCATTCGGGCCATCCATAAGTCTTTCGAACAAGATGTA
Found at i:960831 original size:25 final size:24
Alignment explanation
Indices: 960802--960873 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
960792 TTTTATGTTT
960802 TATGTATTTATTTTATGTATATTAC
1 TATGTATTTATTTTA-GTATATTAC
* *
960827 TATGTGTTTATTTTACGTATATTAT
1 TATGTATTTATTTTA-GTATATTAC
* *
960852 TATATATATTACTTTAGTATAT
1 TATGTAT-TTATTTTAGTATAT
960874 ATTTATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
25 33 0.82
26 7 0.17
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.58
Consensus pattern (24 bp):
TATGTATTTATTTTAGTATATTAC
Found at i:960880 original size:23 final size:26
Alignment explanation
Indices: 960838--960887 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
960828 ATGTGTTTAT
*
960838 TTTACGTATATTATTATATATATTAC
1 TTTACGTATATTATTATATATAATAC
960864 TTTA-GTATA-TATT-TATATAATAC
1 TTTACGTATATTATTATATATAATAC
960887 T
1 T
960888 ACATGTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 4 0.17
25 5 0.22
26 4 0.17
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (26 bp):
TTTACGTATATTATTATATATAATAC
Found at i:961976 original size:271 final size:271
Alignment explanation
Indices: 961493--962027 Score: 944
Period size: 271 Copynumber: 2.0 Consensus size: 271
961483 TCTTTGGTAG
961493 AATAAAAAATTATTTTTATATTGAATTCTTAGGAAAAATTATTATATTCCTTTTATTTCAGTTGG
1 AATAAAAAATTATTTTTATATTGAATTCTTAGGAAAAATTATTATATTCCTTTTATTTCAGTTGG
*
961558 AAAGAGAAATATTTATCCTAAAATATTTTAGGGAGTATTTTCTCTTCAATATGTGAATAATTTCT
66 AAAGAGAAATATTTATCCTAAAATATTTTAAGGAGTATTTTCTCTTCAATATGTGAATAATTTCT
* * **
961623 ATTTCTCCTTAGAATTTTTCATTCAATAATATTGCATGGTTGAATGTGGAATAATGAAATCGTAA
131 ATTTATCCTTAGAAATTTTCATTCAATAATATTGCATGGTTGAATGCAGAATAATGAAATCGTAA
*
961688 TTTATATTTATATTTGAGTTCTTAGATTTCTACTATTAGAGACAATTTATAATCGATAGGTACTA
196 TTTATATTTATATTTGAGTTCTTAGATTTCTACTATTAGAGACAATTTATAATCGATAGGTACCA
961753 ATTTTGAGAGT
261 ATTTTGAGAGT
* *
961764 AATAAAAAATTATTTTTATATTGAATTCTTAGGGAAAATTATTATATTCTTTTTATTTCAGTTGG
1 AATAAAAAATTATTTTTATATTGAATTCTTAGGAAAAATTATTATATTCCTTTTATTTCAGTTGG
* * * *
961829 AAAGATAAATATTTGTCCTAAAGTATTTTAAGGAGTATTTTCTCTTCAATATGTGAATATTTTCT
66 AAAGAGAAATATTTATCCTAAAATATTTTAAGGAGTATTTTCTCTTCAATATGTGAATAATTTCT
*
961894 ATTTATCCTTAGAAATTTTCATTCAATAATATTGCATGGTTGAATGCAGAATAATGGAATCGTAA
131 ATTTATCCTTAGAAATTTTCATTCAATAATATTGCATGGTTGAATGCAGAATAATGAAATCGTAA
*
961959 TTTATATTTATATTTGAGTTCTTAGATTTCTACTATTAGAGACAATTTATAATCGATGGGTACCA
196 TTTATATTTATATTTGAGTTCTTAGATTTCTACTATTAGAGACAATTTATAATCGATAGGTACCA
962024 ATTT
261 ATTT
962028 GAGGCGTTGT
Statistics
Matches: 250, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
271 250 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (271 bp):
AATAAAAAATTATTTTTATATTGAATTCTTAGGAAAAATTATTATATTCCTTTTATTTCAGTTGG
AAAGAGAAATATTTATCCTAAAATATTTTAAGGAGTATTTTCTCTTCAATATGTGAATAATTTCT
ATTTATCCTTAGAAATTTTCATTCAATAATATTGCATGGTTGAATGCAGAATAATGAAATCGTAA
TTTATATTTATATTTGAGTTCTTAGATTTCTACTATTAGAGACAATTTATAATCGATAGGTACCA
ATTTTGAGAGT
Found at i:973744 original size:25 final size:23
Alignment explanation
Indices: 973723--973786 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 23
973713 CATAATATTC
973723 TTTATATATTAACTTAAAAATAT
1 TTTATATATTAACTTAAAAATAT
*
973746 TTT-TATATTAACTTATTAAATAT
1 TTTATATATTAACTTA-AAAATAT
*
973769 ATTATATTATTAACTTAA
1 TTTATA-TATTAACTTAA
973787 TTTAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 12 0.34
23 11 0.31
24 2 0.06
25 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATATATTAACTTAAAAATAT
Found at i:973769 original size:17 final size:17
Alignment explanation
Indices: 973749--973781 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
973739 AAAATATTTT
973749 TATATTA-ACTTATTAAA
1 TATATTATA-TTATTAAA
973766 TATATTATATTATTAA
1 TATATTATATTATTAA
973782 CTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATTATATTATTAAA
Found at i:974555 original size:31 final size:31
Alignment explanation
Indices: 974496--974602 Score: 135
Period size: 31 Copynumber: 3.4 Consensus size: 31
974486 TAATTCGTGA
* *
974496 TGATCACATCTTAATTAAATAAAAAACGAAGG
1 TGATCATATCTTAATTAAAT-AAAAACGAAAG
*
974528 TGATCATATTTTAATTAAATAAAAACGAAAG
1 TGATCATATCTTAATTAAATAAAAACGAAAG
* **
974559 TGATCATATCTTAATAAAATAAAAATAAAAG
1 TGATCATATCTTAATTAAATAAAAACGAAAG
974590 TGA-CTATATCTTA
1 TGATC-ATATCTTA
974603 TTTTTGAAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.01
31 48 0.72
32 18 0.27
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (31 bp):
TGATCATATCTTAATTAAATAAAAACGAAAG
Found at i:975417 original size:5 final size:5
Alignment explanation
Indices: 975407--975434 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
975397 CCTTTTGATG
975407 AAATC AAATC AAATC AAATC AAATC AAA
1 AAATC AAATC AAATC AAATC AAATC AAA
975435 CATTCTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATC
Found at i:976514 original size:31 final size:31
Alignment explanation
Indices: 976479--976538 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
976469 TAAAGTTTGG
*
976479 AAATATTTAGGGACCAAAAGGGTAATTTTCC
1 AAATATTTAGGGACCAAAAGGATAATTTTCC
* *
976510 AAATATTTGGGGACCAAAAGTATAATTTT
1 AAATATTTAGGGACCAAAAGGATAATTTT
976539 TAAAAGTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (31 bp):
AAATATTTAGGGACCAAAAGGATAATTTTCC
Found at i:977255 original size:18 final size:18
Alignment explanation
Indices: 977229--977287 Score: 109
Period size: 18 Copynumber: 3.3 Consensus size: 18
977219 TTACCAAATT
977229 TTAGGGTTTATGTTCATG
1 TTAGGGTTTATGTTCATG
*
977247 TTAGAGTTTATGTTCATG
1 TTAGGGTTTATGTTCATG
977265 TTAGGGTTTATGTTCATG
1 TTAGGGTTTATGTTCATG
977283 TTAGG
1 TTAGG
977288 ATTTTATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.19, C:0.05, G:0.27, T:0.49
Consensus pattern (18 bp):
TTAGGGTTTATGTTCATG
Found at i:979370 original size:19 final size:19
Alignment explanation
Indices: 979339--979390 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
979329 ATGCATTGGT
979339 CTATGAACT-TGAAAATAAA
1 CTATGAA-TATGAAAATAAA
* *
979358 CTATGAATATGAAATTAAG
1 CTATGAATATGAAAATAAA
*
979377 TTATGAATATGAAA
1 CTATGAATATGAAA
979391 TAAGTTATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (19 bp):
CTATGAATATGAAAATAAA
Found at i:979396 original size:18 final size:19
Alignment explanation
Indices: 979359--979400 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
979349 GAAAATAAAC
979359 TATGAATATGAAATTAAGT
1 TATGAATATGAAATTAAGT
979378 TATGAATATGAAA-TAAGT
1 TATGAATATGAAATTAAGT
979396 TATGA
1 TATGA
979401 GTCCGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (19 bp):
TATGAATATGAAATTAAGT
Found at i:979565 original size:18 final size:18
Alignment explanation
Indices: 979542--979606 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
979532 ATGAAAAGAA
979542 TATGATATGACTATTATG
1 TATGATATGACTATTATG
** *
979560 TATGATATTGTTTATCATGG
1 TATGATA-TGACTATTAT-G
*
979580 CTTTGATATGACTATTATG
1 -TATGATATGACTATTATG
979599 TATGATAT
1 TATGATAT
979607 TGTTTATCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 14 0.39
19 8 0.22
20 8 0.22
21 6 0.17
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (18 bp):
TATGATATGACTATTATG
Found at i:979587 original size:39 final size:39
Alignment explanation
Indices: 979544--979626 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
979534 GAAAAGAATA
979544 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
*
979583 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
979622 TGATA
1 TGATA
979627 AAATCATGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
Found at i:989136 original size:14 final size:14
Alignment explanation
Indices: 989117--989144 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
989107 ACAGTCAAGA
989117 GTGTATCGATACAC
1 GTGTATCGATACAC
989131 GTGTATCGATACAC
1 GTGTATCGATACAC
989145 TCGTCAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
GTGTATCGATACAC
Found at i:991858 original size:19 final size:19
Alignment explanation
Indices: 991834--991882 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
991824 GAATGCAATT
991834 AGTGTACCGATGCACCTGG
1 AGTGTACCGATGCACCTGG
991853 AGTGTACCGATGCACCTGG
1 AGTGTACCGATGCACCTGG
991872 AGTGTACCGAT
1 AGTGTACCGAT
991883 ACACTAGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.22
Consensus pattern (19 bp):
AGTGTACCGATGCACCTGG
Found at i:995674 original size:25 final size:26
Alignment explanation
Indices: 995644--995701 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
995634 GAGTACGGAT
995644 TATGAAAATGAAATG-TGAAAACGA-A
1 TATGAAAATGAAA-GATGAAAACGAGA
* *
995669 TATGAAAGTGAAAGATGAAAATGAGA
1 TATGAAAATGAAAGATGAAAACGAGA
995695 TATGAAA
1 TATGAAA
995702 GTTTTGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 20 0.69
26 8 0.28
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (26 bp):
TATGAAAATGAAAGATGAAAACGAGA
Found at i:995699 original size:13 final size:13
Alignment explanation
Indices: 995644--995701 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
995634 GAGTACGGAT
995644 TATGAAAATGAAA
1 TATGAAAATGAAA
* *
995657 TGTGAAAACG-AA
1 TATGAAAATGAAA
*
995669 TATGAAAGTGAAA
1 TATGAAAATGAAA
* *
995682 GATGAAAATGAGA
1 TATGAAAATGAAA
995695 TATGAAA
1 TATGAAA
995702 GTTTTGTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 9 0.26
13 26 0.74
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:999544 original size:28 final size:28
Alignment explanation
Indices: 999512--999570 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 28
999502 TTTACTAGAT
999512 TTTGATTCGATTCAAGCATGAAATCAAC
1 TTTGATTCGATTCAAGCATGAAATCAAC
999540 --T--TT-GATTCAAGCATGAAATCAAC
1 TTTGATTCGATTCAAGCATGAAATCAAC
999563 TTTGATTC
1 TTTGATTC
999571 AACCTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
23 20 0.77
24 2 0.08
25 1 0.04
26 1 0.04
27 2 0.08
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (28 bp):
TTTGATTCGATTCAAGCATGAAATCAAC
Found at i:999550 original size:23 final size:23
Alignment explanation
Indices: 999520--999572 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
999510 ATTTTGATTC
999520 GATTCAAGCATGAAATCAACTTT
1 GATTCAAGCATGAAATCAACTTT
999543 GATTCAAGCATGAAATCAACTTT
1 GATTCAAGCATGAAATCAACTTT
999566 GATTCAA
1 GATTCAA
999573 CCTTATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (23 bp):
GATTCAAGCATGAAATCAACTTT
Found at i:1003846 original size:14 final size:14
Alignment explanation
Indices: 1003824--1003857 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1003814 TTTTTTAAGC
1003824 ATAAT-TTAATATA
1 ATAATATTAATATA
1003837 ATAATATTAATATA
1 ATAATATTAATATA
1003851 ATTAATA
1 A-TAATA
1003858 CTAACTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 9 0.47
15 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATATTAATATA
Found at i:1003851 original size:24 final size:24
Alignment explanation
Indices: 1003824--1003870 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1003814 TTTTTTAAGC
1003824 ATAATTTAATA-TAA-TAATATTAAT
1 ATAA-TTAATACTAACT-ATATTAAT
1003848 ATAATTAATACTAACTATATTAA
1 ATAATTAATACTAACTATATTAA
1003871 GAAATTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 14 0.67
25 1 0.05
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTAATACTAACTATATTAAT
Found at i:1021075 original size:20 final size:20
Alignment explanation
Indices: 1021050--1021117 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
1021040 AGCAAGAGGG
1021050 GTATCGGTACTAGGTGACCA
1 GTATCGGTACTAGGTGACCA
* ** ***
1021070 GTATCGATACCTAGCAAGAGGG
1 GTATCGGTA-CTAG-GTGACCA
1021092 GTATCGGTACTAGGTGACCA
1 GTATCGGTACTAGGTGACCA
1021112 GTATCG
1 GTATCG
1021118 ATACCTAGTG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
20 16 0.47
21 8 0.24
22 10 0.29
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (20 bp):
GTATCGGTACTAGGTGACCA
Found at i:1021095 original size:22 final size:22
Alignment explanation
Indices: 1021028--1021097 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 22
1021018 TATACTAGTA
*
1021028 GTATCGATACATAGCAAGAGGG
1 GTATCGATACCTAGCAAGAGGG
* ** ***
1021050 GTATCGGTA-CTAG-GTGACCA
1 GTATCGATACCTAGCAAGAGGG
1021070 GTATCGATACCTAGCAAGAGGG
1 GTATCGATACCTAGCAAGAGGG
1021092 GTATCG
1 GTATCG
1021098 GTACTAGGTG
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
20 10 0.30
21 7 0.21
22 16 0.48
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.21
Consensus pattern (22 bp):
GTATCGATACCTAGCAAGAGGG
Found at i:1021122 original size:42 final size:42
Alignment explanation
Indices: 1021027--1021125 Score: 189
Period size: 42 Copynumber: 2.4 Consensus size: 42
1021017 CTATACTAGT
*
1021027 AGTATCGATACATAGCAAGAGGGGTATCGGTACTAGGTGACC
1 AGTATCGATACCTAGCAAGAGGGGTATCGGTACTAGGTGACC
1021069 AGTATCGATACCTAGCAAGAGGGGTATCGGTACTAGGTGACC
1 AGTATCGATACCTAGCAAGAGGGGTATCGGTACTAGGTGACC
1021111 AGTATCGATACCTAG
1 AGTATCGATACCTAG
1021126 TGCACAAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.22
Consensus pattern (42 bp):
AGTATCGATACCTAGCAAGAGGGGTATCGGTACTAGGTGACC
Found at i:1030922 original size:30 final size:31
Alignment explanation
Indices: 1030862--1030948 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 31
1030852 AATGGATTTA
* * *
1030862 TTTA-GTGAACAAATTATAAATTTGTTAAAG
1 TTTAGGTGACCAAAATATAAATTTGTAAAAG
*
1030892 TTT-GGTGACCAAACTATAAACTTTG-AAAAG
1 TTTAGGTGACCAAAATATAAA-TTTGTAAAAG
1030922 TTTAGG-GACCAAAATAT-AATTT-TAAAA
1 TTTAGGTGACCAAAATATAAATTTGTAAAA
1030949 AGTTACATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
28 7 0.14
29 2 0.04
30 34 0.69
31 6 0.12
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (31 bp):
TTTAGGTGACCAAAATATAAATTTGTAAAAG
Found at i:1033182 original size:45 final size:45
Alignment explanation
Indices: 1033094--1033251 Score: 244
Period size: 45 Copynumber: 3.4 Consensus size: 45
1033084 GTAACCATGC
*
1033094 AAATAAGCTTACGAGCTTATGGAAATAAATGGTAATTATATTGGTA
1 AAATAAGCTTACGAGCTTATGG-AATAAATGGTAAGTATATTGGTA
* *
1033140 AAATAAGCTTACGAGCTTATGGCATAAATGGTAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1033185 AAATAAGCTTACGAGCTTATGGAATAAATGGTAACTGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA--GTATATTGGTA
* *
1033232 AAATAGGCTTACGAGTTTAT
1 AAATAAGCTTACGAGCTTAT
1033252 AAGATAAATT
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
45 53 0.51
46 22 0.21
47 28 0.27
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1033259 original size:92 final size:91
Alignment explanation
Indices: 1033094--1033260 Score: 266
Period size: 92 Copynumber: 1.8 Consensus size: 91
1033084 GTAACCATGC
1033094 AAATAAGCTTACGAGCTTATGGAAATAAATGGTAATTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGAAATAAATGGTAATTATATTGGTAAAATAAGCTTACGAGCTTA
*
1033159 TGGCATAAATGGTAAGTATATTGGAA
66 TAGCATAAATGGTAAGTATATTGGAA
* *
1033185 AAATAAGCTTACGAGCTTATGG-AATAAATGGTAACTGTATATTGGTAAAATAGGCTTACGAGTT
1 AAATAAGCTTACGAGCTTATGGAAATAAATGGTAA-T-TATATTGGTAAAATAAGCTTACGAGCT
1033249 TATAAG-ATAAAT
64 TAT-AGCATAAAT
1033261 TATAAGAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
90 12 0.17
91 23 0.33
92 34 0.49
93 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (91 bp):
AAATAAGCTTACGAGCTTATGGAAATAAATGGTAATTATATTGGTAAAATAAGCTTACGAGCTTA
TAGCATAAATGGTAAGTATATTGGAA
Found at i:1034753 original size:19 final size:21
Alignment explanation
Indices: 1034714--1034753 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1034704 GACATTTAGA
*
1034714 GTTTCAATTGATGTGGAAAAT
1 GTTTCAATTGATGTCGAAAAT
1034735 GTTTCAATT-AT-TCGAAAAT
1 GTTTCAATTGATGTCGAAAAT
1034754 ATTTTCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (21 bp):
GTTTCAATTGATGTCGAAAAT
Found at i:1035566 original size:106 final size:106
Alignment explanation
Indices: 1035369--1035566 Score: 267
Period size: 106 Copynumber: 1.9 Consensus size: 106
1035359 TTTTAGACGG
* * *
1035369 AATATTAATATCTCTTTATTTCAATTTGGGTAATAAATGACTGTTTTAATGCATGAAGAGTCATT
1 AATAGTAATATCTATTTATTTCAATTTGGGTAATAAATGACTGTTTTAATGCACGAAGAGTCATT
* **
1035434 TATTCTCAATTGGAAATCATCGATATTGAATTTTAAGATGA
66 TATTCTCAATTGGAAATAATAAATATTGAATTTTAAGATGA
*
1035475 AATAGTAATATCTATTTATTTCAA-TTGGAGTAATAAATGATTG-TTTAATGCACGAA-AGGTCA
1 AATAGTAATATCTATTTATTTCAATTTGG-GTAATAAATGACTGTTTTAATGCACGAAGA-GTCA
* *
1035537 TTTTTTCTCGATTGGAAATAATTAAATATT
64 TTTATTCTCAATTGGAAATAA-TAAATATT
1035567 ATCGTTTTCA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
104 1 0.01
105 38 0.47
106 41 0.51
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (106 bp):
AATAGTAATATCTATTTATTTCAATTTGGGTAATAAATGACTGTTTTAATGCACGAAGAGTCATT
TATTCTCAATTGGAAATAATAAATATTGAATTTTAAGATGA
Found at i:1037672 original size:20 final size:21
Alignment explanation
Indices: 1037649--1037694 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
1037639 TTATTGAGTT
*
1037649 GTTAC-AGGTTTAATGCAAGA
1 GTTACAAGCTTTAATGCAAGA
1037669 GTTACAAAGCTTTAATGCAAGA
1 GTTAC-AAGCTTTAATGCAAGA
1037691 GTTA
1 GTTA
1037695 TAGAGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
22 18 0.78
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (21 bp):
GTTACAAGCTTTAATGCAAGA
Found at i:1041997 original size:224 final size:225
Alignment explanation
Indices: 1041599--1042057 Score: 555
Period size: 224 Copynumber: 2.0 Consensus size: 225
1041589 AACATAACCT
* * *
1041599 GTTAATTACTGTAAACATTATCAACCATAATAACATAACAGGTAGTGCTTATGTAACGCAATAAG
1 GTTAATTACTGGAAACATTATCAACCATAATAACATAACAGATAGCGCTTATGTAACGCAATAAG
* *** ** *
1041664 TAGAGTATTTTTAAAGTTGATGATGCCTTAAAAATCTGACAATAACAAATAGGTTAATTACTTGA
66 TAGAGCATTTTTAAAGCAAATGAAACCTTAAAAATCTGACAATAACAAATAGGTTAATTACTTAA
* *
1041729 TTTGTTATCAATATTATCAACATATTAAATAGCGCAAAAAATATTACCAAAGTTTAAGCTGATG-
131 TTTATTATCAATATTATCAACATATTAAATAGCACAAAAAATATTACCAAAGTTTAAGCTGATGA
* **
1041793 GAGCGTTAGAAATCCAATGATAAC-AAATAA
196 GA-CCTTAGAAATCCAACAATAACAAAATAA
* * * * * *
1041823 GTTAATTACTGGAAATATTATCAACTATAATAACATAACA-ATAGCGCTTATTTAATGTAATACG
1 GTTAATTACTGGAAACATTATCAACCATAATAACATAACAGATAGCGCTTATGTAACGCAATAAG
* * * **
1041887 TAGCGCCTTTTTAAAGCAAATGAAACCTTAGAAATCTGATTATAACAAAATAGGTTAATTACTTA
66 TAGAGCATTTTTAAAGCAAATGAAACCTTAAAAATCTGACAATAAC-AAATAGGTTAATTACTTA
* ** *** * *
1041952 ATTTATTATCAATATTATTAACATATTATGTAGCACCTGAAATATTATCAAAGTTTAAGTTGATG
130 ATTTATTATCAATATTATCAACATATTAAATAGCACAAAAAATATTACCAAAGTTTAAGCTGATG
* *
1042017 AGACCTTAGAAATCCGACAATTACAAAATAA
195 AGACCTTAGAAATCCAACAATAACAAAATAA
1042048 GTTAATTACT
1 GTTAATTACT
1042058 TATTTTGTTA
Statistics
Matches: 196, Mismatches: 36, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
223 53 0.27
224 125 0.64
225 18 0.09
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (225 bp):
GTTAATTACTGGAAACATTATCAACCATAATAACATAACAGATAGCGCTTATGTAACGCAATAAG
TAGAGCATTTTTAAAGCAAATGAAACCTTAAAAATCTGACAATAACAAATAGGTTAATTACTTAA
TTTATTATCAATATTATCAACATATTAAATAGCACAAAAAATATTACCAAAGTTTAAGCTGATGA
GACCTTAGAAATCCAACAATAACAAAATAA
Found at i:1042149 original size:106 final size:108
Alignment explanation
Indices: 1041930--1042203 Score: 302
Period size: 106 Copynumber: 2.5 Consensus size: 108
1041920 ATCTGATTAT
* * * * * *
1041930 AACAAAATAGGTTAATTACTTAATTTATTATCAATATTATTAACATATTATGTAGCACCTGAAAT
1 AACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATTAACATATTAGGTAGCACCTAAAAT
* * * *
1041995 ATTATCAAAGTTTAAGTTGATGAGACCTTAGAAATCCGACAAT
66 ATTACCAAAGTTTAAGTTGATGAGACATTAGAAATCCCACAAC
* * * **
1042038 TACAAAATAAGTTAATTACTTATTTTGTTATTAATATTA-TCA-ATATTAGGTAGCGTCTAAAAT
1 AACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATTAACATATTAGGTAGCACCTAAAAT
* * *
1042101 GTTACCAAAGTTTAAGTTGATGAGGCATTCGAAA-CCTCACAAC
66 ATTACCAAAGTTTAAGTTGATGAGACATTAGAAATCC-CACAAC
* * * * *
1042144 AACAAAATATGTTAATTTCTTATTTTGTTATAAATAAATATTAACATACTAGGTTGCACC
1 AACAAAATAAGTTAATTACTTATTTTGTTATAAAT-ATTATTAACATATTAGGTAGCACC
1042204 CAATAATGTT
Statistics
Matches: 135, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
105 2 0.01
106 81 0.60
107 5 0.04
108 36 0.27
109 11 0.08
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (108 bp):
AACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATTAACATATTAGGTAGCACCTAAAAT
ATTACCAAAGTTTAAGTTGATGAGACATTAGAAATCCCACAAC
Found at i:1042752 original size:23 final size:23
Alignment explanation
Indices: 1042681--1042754 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
1042671 ACCGGTAGTT
* * * *
1042681 TATTTAACGTAACAAGTATCACT
1 TATTTAACGTAATAGGTAGCACC
* ***
1042704 TATTTAATGTAATAGGTAGTGTC
1 TATTTAACGTAATAGGTAGCACC
*
1042727 TATTTAACATAATAGGTAGCACC
1 TATTTAACGTAATAGGTAGCACC
1042750 TATTT
1 TATTT
1042755 TATTTTACCA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (23 bp):
TATTTAACGTAATAGGTAGCACC
Found at i:1042816 original size:75 final size:76
Alignment explanation
Indices: 1042729--1042870 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 76
1042719 GTAGTGTCTA
*
1042729 TTTAACATAATAGGTAGCACCTA-TTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAA
1 TTTAACATAATAGGTAGCACCTATTTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAA
1042793 CCGATAGGTAT
66 CCGATAGGTAT
* * *
1042804 TTTAACGTAATAGGTAGCGCCTATTTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAA
1 TTTAACATAATAGGTAGCACCTATTTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAA
1042869 CC
66 CC
1042871 AGTAGACAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 21 0.34
76 41 0.66
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (76 bp):
TTTAACATAATAGGTAGCACCTATTTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAA
CCGATAGGTAT
Found at i:1042884 original size:76 final size:75
Alignment explanation
Indices: 1042729--1042892 Score: 231
Period size: 76 Copynumber: 2.2 Consensus size: 75
1042719 GTAGTGTCTA
*
1042729 TTTAACATAATAGGTAGCACCTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAAC
** *
1042794 CGATAGGTAT
66 CGATAGACAG
* * *
1042804 TTTAACGTAATAGGTAGCGCCTATTTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAA
1 TTTAACATAATAGGTAGCACCTA-TTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAA
1042869 CC-AGTAGACAG
65 CCGA-TAGACAG
*
1042880 TTTAATATAATAG
1 TTTAACATAATAG
1042893 ATATCGCTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 22 0.28
76 56 0.72
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCACCTATTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAAC
CGATAGACAG
Found at i:1042913 original size:23 final size:23
Alignment explanation
Indices: 1042880--1042951 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
1042870 CAGTAGACAG
* * *
1042880 TTTAATATAATAGATATCGCTTA
1 TTTAACATAATAGGTAGCGCTTA
*
1042903 TTTAACGTAATAGGTAGCGCTTA
1 TTTAACATAATAGGTAGCGCTTA
1042926 TTTAACATAATAGGTAGCGCTTA
1 TTTAACATAATAGGTAGCGCTTA
1042949 TTT
1 TTT
1042952 TATTTTACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (23 bp):
TTTAACATAATAGGTAGCGCTTA
Found at i:1042969 original size:197 final size:196
Alignment explanation
Indices: 1042634--1043091 Score: 652
Period size: 197 Copynumber: 2.3 Consensus size: 196
1042624 AAGTTGTATA
* * * * * * * *
1042634 TATTTTACCATTTACATTATAATTAACCTTTAAACAAACCGGTAGTTTA-TTTAACGTAACA-AG
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAACCAGTAG-ATAGTTTAACATAATAGA-
* *
1042697 TATCACTTATTTAATGTAATAGGTAGTGTCTATTTAACATAATAGGTAGCACCTATTTTATTTTA
64 TATCACTTATTTAACGTAATAGGTAGCGTCTATTTAACATAATAGGTAGCACCTATTTTATTTTA
* *
1042762 CCATTTACATTATTAGTAACCTTTAAACAAACCGATAGGTATTTTAACGTAATAGGTAGCGCCTA
129 CCATTTACATTATTACTAACCTTTAAACAAACCGATAGATATTTTAACGTAATAGGTAGCGCCTA
1042827 TTTT
194 -TTT
* *
1042831 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAACCAGTAGACAGTTTAATATAATAGATA
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAACCAGTAGATAGTTTAACATAATAGATA
* * *
1042896 TCGCTTATTTAACGTAATAGGTAGCG-CTTATTTAACATAATAGGTAGCGCTTATTTTATTTTAC
66 TCACTTATTTAACGTAATAGGTAGCGTC-TATTTAACATAATAGGTAGCACCTATTTTATTTTAC
* *
1042960 CGTTTACATTATTACTAACCTTTAAACAAACCGGTAGATATTTTAACGTAATAGGTAGCGCCTAT
130 CATTTACATTATTACTAACCTTTAAACAAACCGATAGATATTTTAACGTAATAGGTAGCGCCTAT
1043025 TT
195 TT
* * * *
1043027 TATTTTACTGCTTACATTATTAGTAACCTTCAAACAAACCAATAGGTAGTTTAACATAATAGATA
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAACCAGTAGATAGTTTAACATAATAGATA
1043092 GATGTTGAAA
Statistics
Matches: 233, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
196 64 0.27
197 168 0.72
198 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (196 bp):
TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAACCAGTAGATAGTTTAACATAATAGATA
TCACTTATTTAACGTAATAGGTAGCGTCTATTTAACATAATAGGTAGCACCTATTTTATTTTACC
ATTTACATTATTACTAACCTTTAAACAAACCGATAGATATTTTAACGTAATAGGTAGCGCCTATT
T
Found at i:1043026 original size:121 final size:122
Alignment explanation
Indices: 1042804--1043026 Score: 331
Period size: 121 Copynumber: 1.8 Consensus size: 122
1042794 CGATAGGTAT
* *
1042804 TTTAACGTAATAGGTAGCGCCTATTTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAA
1 TTTAACATAATAGGTAGCGCCTATTTTTATTTTACCGTTTACATTATTACTAACCTTCAAACAAA
* * *
1042869 CCAGTAGACAGTTTAATATAATAGATATCGCTTATTTAACGTAATAGGTAGCGCTTA
66 CCAGTAGACAGTTTAACATAATAGATAGCGCCTATTTAACGTAATAGGTAGCGCTTA
* *
1042926 TTTAACATAATAGGTAGCGCTTA-TTTTATTTTACCGTTTACATTATTACTAACCTTTAAACAAA
1 TTTAACATAATAGGTAGCGCCTATTTTTATTTTACCGTTTACATTATTACTAACCTTCAAACAAA
* * * * *
1042990 CCGGTAGATATTTTAACGTAATAGGTAGCGCCTATTT
66 CCAGTAGACAGTTTAACATAATAGATAGCGCCTATTT
1043027 TATTTTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
121 68 0.76
122 21 0.24
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (122 bp):
TTTAACATAATAGGTAGCGCCTATTTTTATTTTACCGTTTACATTATTACTAACCTTCAAACAAA
CCAGTAGACAGTTTAACATAATAGATAGCGCCTATTTAACGTAATAGGTAGCGCTTA
Found at i:1043028 original size:75 final size:75
Alignment explanation
Indices: 1042926--1043088 Score: 236
Period size: 75 Copynumber: 2.2 Consensus size: 75
1042916 GTAGCGCTTA
* * *
1042926 TTTAACATAATAGGTAGCGCTTATTTTATTTTACCGTTTACATTATTACTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGCTTACATTATTACTAACCTTCAAACAAAC
1042991 CGGTAGATAT
66 CGGTAGATAT
* * *
1043001 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACTGCTTACATTATTAGTAACCTTCAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGCTTACATTATTACTAACCTTCAAACAAAC
** * *
1043066 CAATAGGTAG
66 CGGTAGATAT
1043076 TTTAACATAATAG
1 TTTAACATAATAG
1043089 ATAGATGTTG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGCTTACATTATTACTAACCTTCAAACAAAC
CGGTAGATAT
Found at i:1043377 original size:28 final size:28
Alignment explanation
Indices: 1043337--1043401 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1043327 TTTTTCAAAG
*
1043337 TGATGCACCGATGTACCAATCCATGCAT
1 TGATGCACCGATGCACCAATCCATGCAT
1043365 TGATGCACCGATGCACCAATCCATGCAT
1 TGATGCACCGATGCACCAATCCATGCAT
*
1043393 CGATGCACC
1 TGATGCACC
1043402 ATGGAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
TGATGCACCGATGCACCAATCCATGCAT
Found at i:1043503 original size:46 final size:45
Alignment explanation
Indices: 1043451--1043562 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 45
1043441 TGCACATACA
*
1043451 ATGCATCGATGCACTTAGGGT-TTTATGAAAACATCGAATGCATT-T
1 ATGCATCGATGCACTAAGGGTATTT-TG-AAACATCGAATGCATTAT
* * * *
1043496 GATGCATCGATGCACTCAGGCTATTTTGGAACATCGAGTGCATTAT
1 -ATGCATCGATGCACTAAGGGTATTTTGAAACATCGAATGCATTAT
1043542 ATGCATCGATGCACTAAGGGT
1 ATGCATCGATGCACTAAGGGT
1043563 CCAACGGTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
45 33 0.57
46 22 0.38
47 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTAAGGGTATTTTGAAACATCGAATGCATTAT
Found at i:1049280 original size:23 final size:23
Alignment explanation
Indices: 1049190--1049292 Score: 85
Period size: 23 Copynumber: 4.7 Consensus size: 23
1049180 TTGTGCTTCA
1049190 TGCATCGAT--ACA-CTT-AATAG
1 TGCATCGATGCACACCTTGAAT-G
*
1049210 TGCATCGATGAATC-CCTTTGAATG
1 TGCATCGATGCA-CACC-TTGAATG
* *
1049234 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
* *
1049255 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
1049278 TGCATCGATGCACAC
1 TGCATCGATGCACAC
1049293 TGCCATGCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
20 9 0.14
21 14 0.21
22 4 0.06
23 24 0.36
24 12 0.18
25 3 0.05
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:1052072 original size:65 final size:62
Alignment explanation
Indices: 1051955--1052162 Score: 197
Period size: 65 Copynumber: 3.2 Consensus size: 62
1051945 TTTCAAAGTG
* * * ** * *
1051955 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATTGAATGAATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATACACTCA-GG-CTATTTTGAAACATCGAATGCATT
1052018 T
62 T
*
1052019 CATGCATCGATGCACATACCATGCATCGATACACTCAGGGT-TTTATGAAAACATCGAATGCATT
1 -ATGCATCGATGCACA-ACCATGCATCGATACACTCAGGCTATTT-TG-AAACATCGAATGCATT
1052083 T
62 T
* *
1052084 GATGCATCGATGCATCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTAT
1 -ATGCATCGATGCA-CAACCATGCATCGATACACTCAGGCTATTTTGAAACATCGAATGCATT-T
*
1052149 ATGCATCGTTGCAC
1 ATGCATCGATGCAC
1052163 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.38
65 66 0.54
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (62 bp):
ATGCATCGATGCACAACCATGCATCGATACACTCAGGCTATTTTGAAACATCGAATGCATTT
Found at i:1053001 original size:75 final size:75
Alignment explanation
Indices: 1052896--1053077 Score: 222
Period size: 75 Copynumber: 2.4 Consensus size: 75
1052886 TAGCGCTTAC
* * * * * *
1052896 TTAACATAATATATAACGCTTATTTTATTTTATCGTTTACATTATTAATAACCTTTAAACAAACC
1 TTAACATAATAGATAACACCTATTTTATTTTACCATTTACATTATTAATAACCTTCAAACAAACC
* *
1052961 GGTGGGTATT
66 GGTAGGTAGT
* * * * *
1052971 TTAACGTACTACG-TAGCACCTATTTTATTTTACCATTTACTTTATTAGTAACCTTCAAACAAAC
1 TTAACATAATA-GATAACACCTATTTTATTTTACCATTTACATTATTAATAACCTTCAAACAAAC
*
1053035 CGGTAGGTGGT
65 CGGTAGGTAGT
1053046 TTAACATAATAGATAACACCTATTTTATTTTA
1 TTAACATAATAGATAACACCTATTTTATTTTA
1053078 ACCGGTTAAG
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
74 1 0.01
75 87 0.99
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (75 bp):
TTAACATAATAGATAACACCTATTTTATTTTACCATTTACATTATTAATAACCTTCAAACAAACC
GGTAGGTAGT
Found at i:1053584 original size:20 final size:20
Alignment explanation
Indices: 1053559--1053602 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1053549 ACCGGATACT
1053559 TTTCAATAACGTTGTGACTA
1 TTTCAATAACGTTGTGACTA
1053579 TTTCAATAACGTTGTGACTA
1 TTTCAATAACGTTGTGACTA
1053599 TTTC
1 TTTC
1053603 GTTGCTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TTTCAATAACGTTGTGACTA
Found at i:1066342 original size:3 final size:3
Alignment explanation
Indices: 1066334--1066383 Score: 55
Period size: 3 Copynumber: 15.0 Consensus size: 3
1066324 TGTCCTGATC
1066334 TTA TTA TTA TTA TTA TTA TTA TTA TATA TATA TATA TATA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA T-TA -TTA TTA
1066381 TTA
1 TTA
1066384 AATAAATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 28 0.62
4 16 0.36
5 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1066945 original size:8 final size:8
Alignment explanation
Indices: 1066932--1066956 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1066922 AATAACGAAT
1066932 GGAAAAGA
1 GGAAAAGA
1066940 GGAAAAGA
1 GGAAAAGA
1066948 GGAAAAGA
1 GGAAAAGA
1066956 G
1 G
1066957 CCTTACCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
GGAAAAGA
Found at i:1070914 original size:42 final size:43
Alignment explanation
Indices: 1070833--1070914 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
1070823 TGGCTTTAGA
* *
1070833 GAAGTTAGGAGTGAAAGTTATCCCCTATATGTAAAGTTTTATT
1 GAAGTTAGGAGTGAAAGCTATCCCCTATATATAAAGTTTTATT
1070876 GAAGTTAGGAGTGAAAGCTAT-CCCTATATATAAAGTTTT
1 GAAGTTAGGAGTGAAAGCTATCCCCTATATATAAAGTTTT
1070915 GTTTGATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 17 0.46
43 20 0.54
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (43 bp):
GAAGTTAGGAGTGAAAGCTATCCCCTATATATAAAGTTTTATT
Found at i:1072765 original size:52 final size:52
Alignment explanation
Indices: 1072698--1072801 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
1072688 TATCAAGATT
1072698 GAAAACCAGATAAACAAGGACCCTTGACCTTACCTCAGAAGAAATATACTCA
1 GAAAACCAGATAAACAAGGACCCTTGACCTTACCTCAGAAGAAATATACTCA
1072750 GAAAACCAGATAAACAAGGACCCTTGACCTTACCTCAGAAGAAATATACTCA
1 GAAAACCAGATAAACAAGGACCCTTGACCTTACCTCAGAAGAAATATACTCA
1072802 AACACTATCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.17
Consensus pattern (52 bp):
GAAAACCAGATAAACAAGGACCCTTGACCTTACCTCAGAAGAAATATACTCA
Found at i:1075215 original size:54 final size:54
Alignment explanation
Indices: 1075131--1075391 Score: 280
Period size: 54 Copynumber: 4.9 Consensus size: 54
1075121 AAATCTGGGT
* * ** *
1075131 AGAAGCCACATG-AAAGAATGAATGTATTGTCAAACATTTTATGAACATCTATGC
1 AGAAGCCACAGGAAAAG-ATGAATGTGTTGTCAAATGTTTTACGAACATCTATGC
* * *
1075185 AGAAGCCACAGGAAAAGATGAATGCGTTGTCAAATGTTTTACAAACAT-T-TGGAA
1 AGAAGCCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTAT-G-C
* *
1075239 AGAAGCCACA-GAAAAGAACGAATGTGTTATCAAATGTTTTACGAACATCTA-GC
1 AGAAGCCACAGGAAAAG-ATGAATGTGTTGTCAAATGTTTTACGAACATCTATGC
* * * * * * *
1075292 TGAAGTCATAGGAAATGATGAATGTGCTGTCAAATGTTTTAAGAACATCTGTGC
1 AGAAGCCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTATGC
* *
1075346 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 AGAAGCCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1075392 CATTGATTAT
Statistics
Matches: 170, Mismatches: 29, Indels: 16
0.79 0.13 0.07
Matches are distributed among these distances:
52 1 0.01
53 44 0.26
54 120 0.71
55 5 0.03
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (54 bp):
AGAAGCCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTATGC
Found at i:1075356 original size:107 final size:108
Alignment explanation
Indices: 1075143--1075391 Score: 306
Period size: 107 Copynumber: 2.3 Consensus size: 108
1075133 AAGCCACATG
* ** *
1075143 AAAGAATGAATGTATTGTCAAACATTTTATGAACATCTATGCAGAAGCCACAGGAAAAGATGAAT
1 AAAGAATGAATGTGTTGTCAAATGTTTTACGAACATCTATGCAGAAGCCACAGGAAAAGATGAAT
* * *
1075208 GCGTTGTCAAATGTTTTACAAACATTTGGAAAGAAGCCACAGA
66 GCGCTGTCAAATGTTTTACAAACATCTGGAAAGAAACCACAGA
* * * * * *
1075251 AAAGAACGAATGTGTTATCAAATGTTTTACGAACATCTA-GCTGAAGTCATAGGAAATGATGAAT
1 AAAGAATGAATGTGTTGTCAAATGTTTTACGAACATCTATGCAGAAGCCACAGGAAAAGATGAAT
* * *
1075315 GTGCTGTCAAATGTTTTA-AGAACATCTGTG-CAGAAACCACAGG
66 GCGCTGTCAAATGTTTTACA-AACATCTG-GAAAGAAACCACAGA
*
1075358 AAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 AAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
1075392 CATTGATTAT
Statistics
Matches: 120, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
106 1 0.01
107 85 0.71
108 34 0.28
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (108 bp):
AAAGAATGAATGTGTTGTCAAATGTTTTACGAACATCTATGCAGAAGCCACAGGAAAAGATGAAT
GCGCTGTCAAATGTTTTACAAACATCTGGAAAGAAACCACAGA
Found at i:1076749 original size:42 final size:42
Alignment explanation
Indices: 1076702--1076787 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
1076692 GTTTCTTAAT
* **
1076702 TTAAAGCCTTCGAGTTATCTGTAAGACCTTCAATGCAAGATG
1 TTAAAGCCTTCGAGTCATCCATAAGACCTTCAATGCAAGATG
* * *
1076744 TTAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATG
1 TTAAAGCCTTCGAGTCATCCATAAGACCTTCAATGCAAGATG
1076786 TT
1 TT
1076788 TTCAAATGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (42 bp):
TTAAAGCCTTCGAGTCATCCATAAGACCTTCAATGCAAGATG
Found at i:1076979 original size:42 final size:42
Alignment explanation
Indices: 1076920--1077005 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
1076910 GTTTATTAAT
* ***
1076920 TTAAAGCCTTTGGGTCATTTGTAAGACCTTCAGTGCAAGATG
1 TTAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAAGATG
* *
1076962 TTAAAGCCTTCGGGTCATCCATAAGACCTTCATTGCAGGATG
1 TTAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAAGATG
1077004 TT
1 TT
1077006 TTCAAATGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (42 bp):
TTAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAAGATG
Found at i:1077016 original size:218 final size:217
Alignment explanation
Indices: 1076487--1077356 Score: 1269
Period size: 218 Copynumber: 4.0 Consensus size: 217
1076477 GCTTAAATTT
* * *
1076487 TTCGGGTCATTTGTTAGACCTTCAGTGCAAGATGTTAAAGCCTTCGAGTCATCCATAAGACCTTC
1 TTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAAGACCTTC
*
1076552 AGTGCATGATGTTTTCAAATGAGATTTTAGAAA-TCAAGCCTCTTAGGGGTTTCTTAATTATCTC
66 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT-AAGCCT-TTAGGGGTTTCTTAATTATCTC
* *
1076616 AAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACCAAGAAACTAAGCTT
129 AAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGGATCCTTGACAACTAAGAAACTAAGC--
* ** *
1076681 GATTTTCAAGAGTTTCTTAATTTAAAGCC
192 ---CTTCGGGGGTTTCTTAATTTAAAGCC
* * *
1076710 TTCGAGTTATCTGTAAGACCTTCAATGCAAGATGTTAAAGCCTTCGGGTCATCCATAAGACCTTC
1 TTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAAGACCTTC
*
1076775 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCA
66 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTT-AGGGGTTTCTTAATTATCTCA
* * *
1076840 AAAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGATCCTTTACAACTAAGAAACTAAGCTTT
130 AAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGGATCCTTGACAACTAAGAAACTAAGCCTT
*
1076905 CGGGGGTTTATTAATTTAAAGCC
195 CGGGGGTTTCTTAATTTAAAGCC
* *
1076928 TTTGGGTCATTTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAAGACCTTC
1 TTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAAGACCTTC
* * *
1076993 ATTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCCTTCAGGGGTTTCTTAATTATCACA
66 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAG-CCTTTAGGGGTTTCTTAATTATCTCA
* *
1077058 AAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGGATCATTTACAACTAAGAAACTAAGCCTT
130 AAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGGATCCTTGACAACTAAGAAACTAAGCCTT
*
1077123 CGGGGGTTTCTTAATTTAAATCC
195 CGGGGGTTTCTTAATTTAAAGCC
* *
1077146 TTCGGGTCATCTGTAAGACCTTCAGTGCAAAATGTTAAAGCCTTCGGGTCATCCATAAAACCTTC
1 TTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAAGACCTTC
* * * *
1077211 AATGCATGATATTTTCAAATGAGATTTTAGAAACCAAGCCTTT-GGGGTTT-TACTAATTATCTC
66 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTAGGGGTTTCT--TAATTATCTC
* * * * * *
1077274 AAAAGTGTTGTTAAATGAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACTAAGAAACCAAGCCT
129 AAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGGATCCTTGACAACTAAGAAACTAAGCCT
*
1077339 TCGGGGGTTTCTTGATTT
194 TCGGGGGTTTCTTAATTT
1077357 GAATTCCAGA
Statistics
Matches: 593, Mismatches: 49, Indels: 16
0.90 0.07 0.02
Matches are distributed among these distances:
215 1 0.00
216 7 0.01
217 87 0.15
218 316 0.53
219 4 0.01
222 2 0.00
223 175 0.30
224 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (217 bp):
TTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAAGACCTTC
AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTAGGGGTTTCTTAATTATCTCAA
AAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGGGATCCTTGACAACTAAGAAACTAAGCCTTC
GGGGGTTTCTTAATTTAAAGCC
Found at i:1077554 original size:3 final size:3
Alignment explanation
Indices: 1077533--1077581 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
1077523 TATCTCGATC
* * * *
1077533 TTA TTT TTA TTA TTG TTA TTA TTA ATA TTA TATA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
1077579 TTA
1 TTA
1077582 AATAAATATT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1077590 original size:25 final size:25
Alignment explanation
Indices: 1077540--1077592 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1077530 ATCTTATTTT
* * *
1077540 TATTATTGTTATTATTAATATTATA
1 TATTATTATTACTATTAATATAATA
1077565 TATTATTATTACTATTAA-ATAA-A
1 TATTATTATTACTATTAATATAATA
1077588 TATTA
1 TATTA
1077593 CAGCCCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 3 0.12
25 16 0.64
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TATTATTATTACTATTAATATAATA
Found at i:1082537 original size:41 final size:41
Alignment explanation
Indices: 1082491--1082578 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
1082481 AGCATTTTCT
*
1082491 AAAAAAAGACCACTAAAATACTAGATTTTAGCGACGTTTGTC
1 AAAAAATG-CCACTAAAATACTAGATTTTAGCGACGTTTGTC
* * * *
1082533 AAAAAATGTCACTAAAGTACTAGGTTTTAGCGGCGTTTGTC
1 AAAAAATGCCACTAAAATACTAGATTTTAGCGACGTTTGTC
*
1082574 TAAAA
1 AAAAA
1082579 CACCACGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 33 0.82
42 7 0.17
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (41 bp):
AAAAAATGCCACTAAAATACTAGATTTTAGCGACGTTTGTC
Found at i:1083524 original size:15 final size:15
Alignment explanation
Indices: 1083487--1083526 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1083477 ATATTTTTTA
1083487 TTATTGGAGTCGTTG
1 TTATTGGAGTCGTTG
* *
1083502 TCAATGGAGTCGTTG
1 TTATTGGAGTCGTTG
1083517 TTATTGGAGT
1 TTATTGGAGT
1083527 ATTGGGGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.07, G:0.33, T:0.42
Consensus pattern (15 bp):
TTATTGGAGTCGTTG
Found at i:1084056 original size:22 final size:24
Alignment explanation
Indices: 1084000--1084056 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1083990 TATCTTATGT
* *
1084000 TAAAATGTTTATTTTATATTACTA
1 TAAAATATTTATTTTATATCACTA
*
1084024 TGAAATATTTATTTTA-ATCA-TA
1 TAAAATATTTATTTTATATCACTA
*
1084046 TAAAATTTTTA
1 TAAAATATTTA
1084057 AGTCACTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 11 0.39
23 3 0.11
24 14 0.50
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
TAAAATATTTATTTTATATCACTA
Found at i:1091496 original size:15 final size:15
Alignment explanation
Indices: 1091476--1091508 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1091466 TATGTTGGGT
*
1091476 CATTCGATATGGGGC
1 CATTCGATATGGAGC
1091491 CATTCGATATGGAGC
1 CATTCGATATGGAGC
1091506 CAT
1 CAT
1091509 AGAAATAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (15 bp):
CATTCGATATGGAGC
Found at i:1094399 original size:137 final size:138
Alignment explanation
Indices: 1094152--1094410 Score: 380
Period size: 137 Copynumber: 1.9 Consensus size: 138
1094142 GAAGAGATGG
* ** *
1094152 AATGGAAATTCACAAACTTATTATGAATTTCATGGATTCACACATAGTGCCGAAAGGACACACAA
1 AATGGAAATTCACAAACTCATTATGAATACCATGGATTCACACATAGTGCCAAAAGGACACACAA
1094217 TACTAATACAAAAATGCACCCTTATGAATTAAACAAAATCGATCGATAACTTTTATACATAATTA
66 TACTAATACAAAAATGCACCCTTATGAATTAAACAAAATCGATCGATAACTTTTATACATAATTA
1094282 TTTATCGA
131 TTTATCGA
* * * *
1094290 AATGGTAATTCACAAACTCATTATGAATACCAT-GATTGCACATC-TATTGCTAAAAGTACACA-
1 AATGGAAATTCACAAACTCATTATGAATACCATGGATT-CACA-CATAGTGCCAAAAGGACACAC
* * *
1094352 AATACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACTTTTATA
64 AATACTAATACAAAAATGCACCCTTATGAATTAAACAAAATCGATCGATAACTTTTATA
1094411 AACAATTTAT
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
137 60 0.56
138 47 0.44
139 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (138 bp):
AATGGAAATTCACAAACTCATTATGAATACCATGGATTCACACATAGTGCCAAAAGGACACACAA
TACTAATACAAAAATGCACCCTTATGAATTAAACAAAATCGATCGATAACTTTTATACATAATTA
TTTATCGA
Found at i:1094932 original size:20 final size:20
Alignment explanation
Indices: 1094907--1094978 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
1094897 AGGCTAAATA
*
1094907 GTATCGGTACCCTTTCTATG
1 GTATCGATACCCTTTCTATG
1094927 GTATCGATACCCTTTCTATG
1 GTATCGATACCCTTTCTATG
* *
1094947 GTATCGATACTTCTATACTATG
1 GTATCGATAC-CCT-TTCTATG
1094969 GTATCGATAC
1 GTATCGATAC
1094979 TCCCTTCAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 29 0.62
21 2 0.04
22 16 0.34
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (20 bp):
GTATCGATACCCTTTCTATG
Done.