Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000402.1 Hibiscus syriacus cultivar Beakdansim tig00000738_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: 1701760
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:490351 original size:11 final size:11
Alignment explanation
Indices: 490325--490360 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
490315 AACCAAAGAA
490325 AAAAATCAAAG
1 AAAAATCAAAG
490336 CAAAAATCAAAG
1 -AAAAATCAAAG
*
490348 AAAAAGCAAAG
1 AAAAATCAAAG
490359 AA
1 AA
490361 CAAAAGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.06
Consensus pattern (11 bp):
AAAAATCAAAG
Found at i:491541 original size:4 final size:4
Alignment explanation
Indices: 491532--491569 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
491522 CGAGAAAAGT
* *
491532 ATAC ATAC ATAC ACAC ACAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
491570 CCATGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAC
Found at i:492245 original size:103 final size:103
Alignment explanation
Indices: 492034--492271 Score: 268
Period size: 103 Copynumber: 2.3 Consensus size: 103
492024 TGAGAATTTT
* * *
492034 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* **
492099 AAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTT
66 AAAACAAAATTAATCTCACCTTAGATCGTTGTTTCTAA
* * * *
492137 CAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAC-
* * * *
492202 TTAAACAAAGTTGATTTCA-CTTGAGATCG-T-TTTCTCAA
65 TAAAACAAAATTAATCTCACCTT-AGATCGTTGTTTCT-AA
* *
492240 AAAAC-AATCTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAAT-TTCGTCTCGCTTGAGACATTTTC
492272 TCTAAAAACA
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
102 8 0.07
103 85 0.75
104 20 0.18
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (103 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAACAAAATTAATCTCACCTTAGATCGTTGTTTCTAA
Found at i:492279 original size:36 final size:36
Alignment explanation
Indices: 492232--492336 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 36
492222 TTGAGATCGT
*
492232 TTTCTCAAAAAAC-AATCTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAAT-TTTGTCTCGCTTGAGACAA
** *
492268 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
492304 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
492337 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
34 22 0.38
35 1 0.02
36 32 0.55
37 3 0.05
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:492649 original size:29 final size:29
Alignment explanation
Indices: 492577--492665 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 29
492567 ACAGTTTCTC
492577 TTGAA-AAAAATCTTTGG-GTTTGTTCCTT
1 TTGAATAAAAATC-TTGGAGTTTGTTCCTT
492605 TTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAATAAAAATCTTGGAGTTTGTTCCTT
* * *
492634 TTGAATAAATATCTT-GAG-TCGTTTCTT
1 TTGAATAAAAATCTTGGAGTTTGTTCCTT
492661 TTGAA
1 TTGAA
492666 AATCTTTGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
27 12 0.21
28 12 0.21
29 32 0.57
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (29 bp):
TTGAATAAAAATCTTGGAGTTTGTTCCTT
Found at i:492802 original size:26 final size:27
Alignment explanation
Indices: 492773--492837 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
492763 GACAATTTTG
492773 TGAAAAAAATCTTTGAG-ATGTTTCTT
1 TGAAAAAAATCTTTGAGTATGTTTCTT
*
492799 TGAAAAAAATCTTTGAGTTTGTTTCTT
1 TGAAAAAAATCTTTGAGTATGTTTCTT
492826 TGGAAACAAAAT
1 T-GAAA-AAAAT
492838 TTTTTCTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 17 0.49
27 9 0.26
28 4 0.11
29 5 0.14
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (27 bp):
TGAAAAAAATCTTTGAGTATGTTTCTT
Found at i:492846 original size:89 final size:93
Alignment explanation
Indices: 492739--492906 Score: 229
Period size: 89 Copynumber: 1.8 Consensus size: 93
492729 TCTTGAGTCT
* *
492739 GAAACAAAGTTTTGTCTCTCTTGAGACAATTT-TGTG-AA-AAAAATCTTTGAG-ATGTTTCTTT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTTCTGTGAAACAAAAATCTTTGAGTATGTTTCTTT
492800 GAAA-AAAATCTTTGAGTTTGTTTCTTTG
66 GAAACAAAAT-TTTGAGTTTGTTTCTTTG
* * * * *
492828 GAAACAAAATTTTTTCTCTCTTAAGATAGTTTCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTTCTGTGAAACAAAAATCTTTGAGTATGTTTCTTT
492893 GAAACAAAATTTTG
66 GAAACAAAATTTTG
492907 TCTCTCTTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
89 27 0.40
90 3 0.04
91 2 0.03
92 13 0.19
93 17 0.25
94 5 0.07
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (93 bp):
GAAACAAAATTTTGTCTCTCTTAAGACAATTTCTGTGAAACAAAAATCTTTGAGTATGTTTCTTT
GAAACAAAATTTTGAGTTTGTTTCTTTG
Found at i:492861 original size:37 final size:35
Alignment explanation
Indices: 492819--492938 Score: 117
Period size: 29 Copynumber: 3.5 Consensus size: 35
492809 CTTTGAGTTT
492819 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATA
1 GTTTCTTT-GAAACAAAA-TTTTTCTCTCTTAAGATA
* * * *
492856 GTTTCTTTGAAACAAAA-----ATCT-TTGAGTTT
1 GTTTCTTTGAAACAAAATTTTTCTCTCTTAAGATA
492885 GTTTCTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
492921 ATTTCTTTTGAAACAAAA
1 GTTTC-TTTGAAACAAAA
492939 ATCTTTGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
29 22 0.33
30 3 0.05
35 3 0.05
36 18 0.27
37 20 0.30
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (35 bp):
GTTTCTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:492918 original size:65 final size:66
Alignment explanation
Indices: 492788--492956 Score: 265
Period size: 66 Copynumber: 2.6 Consensus size: 66
492778 AAAATCTTTG
*
492788 AGAT-GTTTCTTTG-AA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTT
1 AGATAGTTTCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTT
492850 A
66 A
492851 AGATAGTTTCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTT-GAAACAAAATTTTGTCTCTCTT
1 AGATAGTTTCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTT
492915 A
66 A
* * *
492916 AGATAATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCT
1 AGATAGTTTC-TTTGAAACAAAAATCTTTGAGTTTGTTTCT
492957 CTTAAAATGA
Statistics
Matches: 98, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
63 4 0.04
64 9 0.09
65 33 0.34
66 52 0.53
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (66 bp):
AGATAGTTTCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTT
A
Found at i:492970 original size:66 final size:66
Alignment explanation
Indices: 492788--492998 Score: 247
Period size: 66 Copynumber: 3.3 Consensus size: 66
492778 AAAATCTTTG
* * *
492788 AGAT-GTTTC-TTTG-AA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTT-GAAACAAAATTTTGTCTCTCT
492849 TA
65 TA
* *
492851 AGATAGTTTC-TTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGAAACAAAATTTTGTCTCTCTT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTTGAAACAAAATTTTGTCTCTCTT
492915 A
66 A
* * *
492916 AGATAATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTATCTC
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCT-TTGAAACA-AAATTTTGTCTCTC
*
492979 TTG
64 TTA
**
492982 AGACCGTTTCTTTTGAA
1 AGATAGTTTCTTTTGAA
492999 GTAAATCTTT
Statistics
Matches: 132, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
63 4 0.03
64 9 0.07
65 34 0.26
66 83 0.63
67 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (66 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTTGAAACAAAATTTTGTCTCTCTT
A
Found at i:493231 original size:120 final size:119
Alignment explanation
Indices: 493057--493280 Score: 258
Period size: 120 Copynumber: 1.9 Consensus size: 119
493047 TTAACAAAAT
* * **
493057 CATCTTTGAGTCAATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACGGTTTCTAATGAAAAAC
1 CATCTTTGAGTCAATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAA-
493122 TAA-CTTTTGAGAGTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGAGATC
65 -AATC-TTTGAGAGTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGAGATC
* ** **
493177 CATCTTTGAGTCAGTTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAAA
1 CATCTTTGAGTCAATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATGAAAA
** * *
493240 AAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
64 AAATCTTTGAGAGTGTTTCATTTGAAACAAAATTTGGTCTC
493281 TCGAGACAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
118 22 0.25
119 19 0.22
120 42 0.48
121 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (119 bp):
CATCTTTGAGTCAATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAAA
ATCTTTGAGAGTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGAGATC
Found at i:493258 original size:64 final size:64
Alignment explanation
Indices: 493178--493534 Score: 198
Period size: 64 Copynumber: 5.6 Consensus size: 64
493168 GATGAGATCC
** *
493178 ATCTTTGAGTCAGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAAAAAA
* ** *
493242 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC-TCGAGACAACTTC-TTTGAAAATAC
1 ATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAAAA-A-
*
493305 CC
64 -A
* * * * * ** * * * * ** *
493307 ACCTTTGAGATTGTTTCTATTAAAAC-TAATTTTGTCTCGCATGAGAC-AGTTCCTTTCAATGAC
1 ATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTTA-AAGACAATTTCTTTTGAAAAAA
* ** * * * * *
493370 ATCTTTGAG-TCGTTTCCCTTCAAAC-GAATTTTGTCTCTTGAA-AC-ATTTCTCTTAAAATAAG
1 ATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAAA-AA-
493431 A
64 A
* * ** * * *
493432 TCATCTTTGAGTTTGTTTCTCTGGAAACAAGGTTTTATCCCTTAAA-ACAGTTTCTTTTGAAGAA
1 --ATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAA-AA
493496 AA
63 AA
*
493498 ATC--TGAGTCTGTTTC-TTTGAAAACAAAATTTTGTCTC
1 ATCTTTGAGTTTGTTTCTTTTG-AAACAAAATTTTGTCTC
493535 ACTAAGATAC
Statistics
Matches: 221, Mismatches: 57, Indels: 32
0.71 0.18 0.10
Matches are distributed among these distances:
60 10 0.05
61 4 0.02
62 55 0.25
63 20 0.09
64 58 0.26
65 38 0.17
66 24 0.11
67 11 0.05
68 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (64 bp):
ATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTTAAAGACAATTTCTTTTGAAAAAA
Found at i:493714 original size:35 final size:35
Alignment explanation
Indices: 493685--493758 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
493675 TGTTTCTTTG
* *
493685 GAAACAAAATTACCATCTTTGAATATGTTTCCCTT
1 GAAACAAAATAAACATCTTTGAATATGTTTCCCTT
* *
493720 GAAACAAAATAAACATCTTTGAGAT-CGTTTACCTT
1 GAAACAAAATAAACATCTTTGA-ATATGTTTCCCTT
493755 GAAA
1 GAAA
493759 TGAATTTCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.94
36 2 0.06
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (35 bp):
GAAACAAAATAAACATCTTTGAATATGTTTCCCTT
Found at i:494323 original size:129 final size:127
Alignment explanation
Indices: 494111--494388 Score: 470
Period size: 129 Copynumber: 2.2 Consensus size: 127
494101 CCAGCCGTCC
* *
494111 TCATCATGTAGGAACCGTGTCATCCCCAGACCATCTCCTTATCACGTAGGAGCCGTGTCAACCAT
1 TCATCACGTAGGAGCCGTGTCATCCCCAGACCATCTCCTTATCACGTAGGAGCCGTGTCAACCAT
*
494176 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
*
494238 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCT-CTTCATCACGTAGGAGCCGTGTCAA
1 TCATCACGTAGGAGCCGTGTCA-TCCCCAGACC--ATCTCCTT-ATCACGTAGGAGCCGTGTCAA
494301 CCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTC
62 CCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTC
494366 T
127 T
494367 TCATCACGTAGGAGCCGTGTCA
1 TCATCACGTAGGAGCCGTGTCA
494389 ACCATAGATA
Statistics
Matches: 142, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
127 23 0.16
128 8 0.06
129 111 0.78
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (127 bp):
TCATCACGTAGGAGCCGTGTCATCCCCAGACCATCTCCTTATCACGTAGGAGCCGTGTCAACCAT
AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:494376 original size:89 final size:89
Alignment explanation
Indices: 494268--494476 Score: 357
Period size: 89 Copynumber: 2.4 Consensus size: 89
494258 CATTCCCCGA
* *
494268 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGG
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
494333 AACCATGTTATCACCTTTAGATGG
66 AACCATGTTATCACCTTTAGATGG
* *
494357 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCATGTAGG
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
*
494422 AACCGTGTTATCACCTTTAGATGG
66 AACCATGTTATCACCTTTAGATGG
*
494446 CCAGAACTC-TCATCACGTATGAGCCGTGTCA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA
494477 TTCCCGACCA
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
88 21 0.18
89 93 0.82
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (89 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
AACCATGTTATCACCTTTAGATGG
Found at i:494505 original size:127 final size:128
Alignment explanation
Indices: 494357--494604 Score: 435
Period size: 127 Copynumber: 1.9 Consensus size: 128
494347 CTTTAGATGG
* *
494357 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCATGTAGG
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
* *
494422 AACCGTGTTATCACCTTTAGATGGCCAGAACTC-TCATCACGTATGAGCCGTGTCATTCCCGA
66 AACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCATTCCCGA
* *
494484 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGG
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
494549 AACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCA
66 AACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCA
494605 ACCATAGATA
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
127 93 0.82
128 21 0.18
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (128 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
AACCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCATTCCCGA
Found at i:494559 original size:216 final size:218
Alignment explanation
Indices: 494151--494694 Score: 1029
Period size: 216 Copynumber: 2.5 Consensus size: 218
494141 CCATCTCCTT
* *
494151 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
1 ATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCACGTAGGAACCGTGTTATC
494216 ACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCA
66 ACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCA
494281 TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
131 TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
494346 CCTTTAGATGGCCAGAACTCTTC
196 CCTTTAGATGGCCAGAACTCTTC
*
494369 ATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCATGTAGGAACCGTGTTATC
1 ATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCACGTAGGAACCGTGTTATC
494434 ACCTTTAGATGGCCAGAACTC-TCATCACGTATGAGCCGTGTCATT-CCCGACCAGATCTCTTCA
66 ACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCA
494497 TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
131 TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
494562 CCTTTAGATGGCCAGAACTCTTC
196 CCTTTAGATGGCCAGAACTCTTC
494585 ATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCACGTAGGAACCGTGTTATC
1 ATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCACGTAGGAACCGTGTTATC
*
494650 ACCTTTAGATGGCCAAGAACTCTTCATCACGTAGGAGCCGTGTCA
66 ACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTCA
494695 CCTTTAGACG
Statistics
Matches: 319, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
216 184 0.58
217 31 0.10
218 104 0.33
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (218 bp):
ATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCACGTAGGAACCGTGTTATC
ACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCA
TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
CCTTTAGATGGCCAGAACTCTTC
Found at i:494635 original size:89 final size:89
Alignment explanation
Indices: 494484--494694 Score: 377
Period size: 89 Copynumber: 2.4 Consensus size: 89
494474 TCATTCCCGA
* *
494484 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGG
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
494549 AACCATGTTATCACCTTTAGATGG
66 AACCATGTTATCACCTTTAGATGG
*
494573 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCGTCACGTAGG
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
*
494638 AACCGTGTTATCACCTTTAGATGG
66 AACCATGTTATCACCTTTAGATGG
494662 CCAAGAACTCTTCATCACGTAGGAGCCGTGTCA
1 CC-AGAACTCTTCATCACGTAGGAGCCGTGTCA
494695 CCTTTAGACG
Statistics
Matches: 117, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 87 0.74
90 30 0.26
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (89 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAAACAGCCGTCCTCATCACGTAGG
AACCATGTTATCACCTTTAGATGG
Found at i:494725 original size:43 final size:43
Alignment explanation
Indices: 494151--494736 Score: 293
Period size: 43 Copynumber: 13.4 Consensus size: 43
494141 CCATCTCCTT
* * *
494151 ATCACGTAGGAGCCGTGTCAACCATAGAT-AACCAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTC-ACCTTAGATGAACCAGAAC-TCTTC
* *
494194 ATCACGTAGGAACCGTGTTATCACCTTTAGATG-GCCAGAACTCTTC
1 ATCACGTAGGAGCCGTG---TCACC-TTAGATGAACCAGAACTCTTC
* **** *
494240 ATCACGTATGAGCCGTGTCA--TTCCCCG-ACCAGATCTCTTC
1 ATCACGTAGGAGCCGTGTCACCTTAGATGAACCAGAACTCTTC
* * *
494280 ATCACGTAGGAGCCGTGTCAACCATAGAT-AACCAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTC-ACCTTAGATGAACCAGAAC-TCTTC
* * *
494323 ATCACGTAGGAACCATGTTATCACCTTTAGATG-GCCAGAACTCTTC
1 ATCACGTAGGAGCC--G-TGTCACC-TTAGATGAACCAGAACTCTTC
* * * *
494369 ATCACGTAGGAGCCGTGTCAACCATAGAT-AAACAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTC-ACCTTAGATGAACCAGAAC-TCTTC
* * * *
494412 GTCATGTAGGAACCGTGTTATCACCTTTAGATG-GCCAGAACTC-TC
1 ATCACGTAGGAGCCGTG---TCACC-TTAGATGAACCAGAACTCTTC
* *** *
494457 ATCACGTATGAGCCGTGTCA--TT-CCCG-ACCAGATCTCTTC
1 ATCACGTAGGAGCCGTGTCACCTTAGATGAACCAGAACTCTTC
* * *
494496 ATCACGTAGGAGCCGTGTCAACCATAGAT-AACCAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTC-ACCTTAGATGAACCAGAAC-TCTTC
* * *
494539 ATCACGTAGGAACCATGTTATCACCTTTAGATG-GCCAGAACTCTTC
1 ATCACGTAGGAGCC--G-TGTCACC-TTAGATGAACCAGAACTCTTC
* * * *
494585 ATCACGTAGGAGCCGTGTCAACCATAGAT-AAACAG-CCGTCCTC
1 ATCACGTAGGAGCCGTGTC-ACCTTAGATGAACCAGAAC-TCTTC
* * *
494628 GTCACGTAGGAACCGTGTTATCACCTTTAGATG-GCCAAGAACTCTTC
1 ATCACGTAGGAGCCGTG---TCACC-TTAGATGAACC-AGAACTCTTC
* *
494675 ATCACGTAGGAGCCGTGTCACCTTTAGACGACCCA-AACTCTTC
1 ATCACGTAGGAGCCGTGTCACC-TTAGATGAACCAGAACTCTTC
* *
494718 ATCACGTATGAGCAGTGTC
1 ATCACGTAGGAGCCGTGTC
494737 GTCCCCAACA
Statistics
Matches: 410, Mismatches: 83, Indels: 100
0.69 0.14 0.17
Matches are distributed among these distances:
38 9 0.02
39 22 0.05
40 33 0.08
41 1 0.00
42 8 0.02
43 148 0.36
44 21 0.05
45 34 0.08
46 108 0.26
47 25 0.06
48 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
ATCACGTAGGAGCCGTGTCACCTTAGATGAACCAGAACTCTTC
Found at i:494906 original size:3 final size:3
Alignment explanation
Indices: 494893--494935 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
494883 TTTTTTATCG
* *
494893 TTA TT- TTA TTA TTA TTA TTA TTA TTT TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
494936 CATATTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:494916 original size:20 final size:20
Alignment explanation
Indices: 494896--494935 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
494886 TTTATCGTTA
*
494896 TTTTATTATTATTATTATTAT
1 TTTTA-TATTATTAATATTAT
494917 TTTTATATTATTAATATTA
1 TTTTATATTATTAATATTA
494936 CATATTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATATTATTAATATTAT
Found at i:495037 original size:25 final size:25
Alignment explanation
Indices: 495008--495055 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
494998 CCAACCCATC
495008 AGATTAGGGTTTCAAACCCTAAACT
1 AGATTAGGGTTTCAAACCCTAAACT
495033 AGATTAGGGTTTCAAACCCTAAA
1 AGATTAGGGTTTCAAACCCTAAA
495056 TGTTCCAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAACT
Found at i:506480 original size:14 final size:14
Alignment explanation
Indices: 506461--506487 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
506451 TTGAACATGG
506461 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
506475 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
506488 TAAAAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:506682 original size:17 final size:19
Alignment explanation
Indices: 506660--506694 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
506650 GCTTTTGTTC
506660 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
506677 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
506695 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:513964 original size:21 final size:22
Alignment explanation
Indices: 513897--513948 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
513887 AGATTGCTGC
513897 CAGGGAACCGATTCCCCTGCTA
1 CAGGGAACCGATTCCCCTGCTA
513919 CAGGGAACCGATTCCCCTGCTA
1 CAGGGAACCGATTCCCCTGCTA
513941 CAGGGAAC
1 CAGGGAAC
513949 TGATACCCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (22 bp):
CAGGGAACCGATTCCCCTGCTA
Found at i:514052 original size:21 final size:21
Alignment explanation
Indices: 514015--514056 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
514005 GGTCATCTCT
*
514015 ATACATTTACCATTTACAAAA
1 ATACATTTAACATTTACAAAA
514036 ATACATTTAAACA-TTACAAAA
1 ATACATTT-AACATTTACAAAA
514057 CTTGTTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (21 bp):
ATACATTTAACATTTACAAAA
Found at i:514742 original size:31 final size:31
Alignment explanation
Indices: 514703--514783 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
514693 AACCTCGACA
* * *
514703 ACTGTCCATAGGTCCCGAAGAACCTAGGTA-
1 ACTGTCCATATGTCCCGAAGAACATAAGTAT
* **
514733 ATCTGTCCATATGTTCCTTAGAACATAAGTAT
1 A-CTGTCCATATGTCCCGAAGAACATAAGTAT
514765 ACTGTCCATATGTCCCGAA
1 ACTGTCCATATGTCCCGAA
514784 AGACATAGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAAGTAT
Found at i:531864 original size:17 final size:19
Alignment explanation
Indices: 531844--531878 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
531834 TTTAGAATTA
531844 TTAATTAT-TT-TTTTGTG
1 TTAATTATATTATTTTGTG
531861 TTAATTATATTATTTTGT
1 TTAATTATATTATTTTGT
531879 CTACAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (19 bp):
TTAATTATATTATTTTGTG
Found at i:532101 original size:13 final size:13
Alignment explanation
Indices: 532083--532129 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
532073 AAATATTTTC
532083 AATATATTTATTT
1 AATATATTTATTT
* *
532096 AATATA-ATAATT
1 AATATATTTATTT
*
532108 AATATATTTATTC
1 AATATATTTATTT
532121 AATATATTT
1 AATATATTT
532130 TCATGTTCTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATATTTATTT
Found at i:534223 original size:19 final size:19
Alignment explanation
Indices: 534181--534223 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
534171 ATATTATATA
** *
534181 TATATAATATATACTTATG
1 TATATAATATATAAGTATC
*
534200 AATATAATATATAAGTATC
1 TATATAATATATAAGTATC
534219 TATAT
1 TATAT
534224 GCATATATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
TATATAATATATAAGTATC
Found at i:534351 original size:20 final size:18
Alignment explanation
Indices: 534326--534362 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
534316 TATATACATA
534326 TATACTTATATAATTATATG
1 TATACTTAT-T-ATTATATG
534346 TATACTTATTATTATAT
1 TATACTTATTATTATAT
534363 TTAAATCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
TATACTTATTATTATATG
Found at i:548213 original size:21 final size:21
Alignment explanation
Indices: 548189--548229 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
548179 CGTTGTTGGA
*
548189 GGAGGAAGAGGAAGAGGAAGT
1 GGAGGAAGAAGAAGAGGAAGT
*
548210 GGAGGAAGAAGAGGAGGAAG
1 GGAGGAAGAAGAAGAGGAAG
548230 AGTCGGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.02
Consensus pattern (21 bp):
GGAGGAAGAAGAAGAGGAAGT
Found at i:548225 original size:12 final size:12
Alignment explanation
Indices: 548186--548230 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
548176 CTCCGTTGTT
*
548186 GGAGGAGGAAGA
1 GGAGGAAGAAGA
* * *
548198 GGAAGAGGAAGT
1 GGAGGAAGAAGA
548210 GGAGGAAGAAGA
1 GGAGGAAGAAGA
548222 GGAGGAAGA
1 GGAGGAAGA
548231 GTCGGAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.53, T:0.02
Consensus pattern (12 bp):
GGAGGAAGAAGA
Found at i:549392 original size:106 final size:106
Alignment explanation
Indices: 549207--549524 Score: 615
Period size: 106 Copynumber: 3.0 Consensus size: 106
549197 TACATATTCA
549207 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
1 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
549272 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
66 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
549313 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
1 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
549378 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
66 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
549419 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
1 TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
549484 TAT-GGATTCTTTTTCTTTGCGAA-T-TGATTTAGTTACTG
66 TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
549522 TAT
1 TAT
549525 GATTCTGTTG
Statistics
Matches: 212, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
103 17 0.08
104 1 0.00
105 20 0.09
106 174 0.82
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (106 bp):
TATCTGTTACTAGTTATTCTGGGATTTATTGAGTGGGAGTCTAACAGAATAGCCTAGAAGCATAT
TATGGGATTCTTTTTCTTTGCGAATTGTGATTTAGTTACTG
Found at i:554544 original size:18 final size:18
Alignment explanation
Indices: 554518--554562 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
554508 TCACGGAATG
* *
554518 TAAGATTACCGGCGGTAA
1 TAAGATTACCGGAGGGAA
*
554536 TAGGATTACCGGAGGGAA
1 TAAGATTACCGGAGGGAA
554554 TAAGATTAC
1 TAAGATTAC
554563 TGGGAATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (18 bp):
TAAGATTACCGGAGGGAA
Found at i:556851 original size:15 final size:14
Alignment explanation
Indices: 556831--556875 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
556821 GGCAACTCAT
556831 TTTATTATTTTTTTA
1 TTTATT-TTTTTTTA
*
556846 TTTATTTTTTGGTTA
1 TTTATTTTTT-TTTA
*
556861 TTTATTTTTCTTTA
1 TTTATTTTTTTTTA
556875 T
1 T
556876 ATTTTTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (14 bp):
TTTATTTTTTTTTA
Found at i:558298 original size:30 final size:29
Alignment explanation
Indices: 558250--558335 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 29
558240 TTTTACCAAC
*
558250 ATTTTTTCTAACATTTGTTATTAAGGGTCT
1 ATTTTTTC-AATATTTGTTATTAAGGGTCT
* * *
558280 AATTTTTTCAATACTTGTTATTATGGGCCT
1 -ATTTTTTCAATATTTGTTATTAAGGGTCT
* *
558310 -TTTTTTTAATATTTGTTATTAGGGGT
1 ATTTTTTCAATATTTGTTATTAAGGGT
558336 ATACTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 22 0.47
30 17 0.36
31 8 0.17
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (29 bp):
ATTTTTTCAATATTTGTTATTAAGGGTCT
Found at i:558325 original size:28 final size:28
Alignment explanation
Indices: 558251--558330 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 28
558241 TTTACCAACA
* * *
558251 TTTTTTCTAACATTTGTTATTAAGGGTC
1 TTTTTTTTAATATTTGTTATTAAGGGCC
* * *
558279 TAATTTTTTCAATACTTGTTATTATGGGCC
1 T--TTTTTTTAATATTTGTTATTAAGGGCC
558309 TTTTTTTTAATATTTGTTATTA
1 TTTTTTTTAATATTTGTTATTA
558331 GGGGTATACT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 20 0.48
30 22 0.52
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (28 bp):
TTTTTTTTAATATTTGTTATTAAGGGCC
Found at i:560423 original size:29 final size:29
Alignment explanation
Indices: 560390--560451 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
560380 TGAACATATA
* *
560390 AATAGTCGAGTGATCATTTTATATCTTTT
1 AATAGTCGAGAGATCATTTTATAACTTTT
*
560419 AATAGTTGAGAGATCATTTTATAACTTTT
1 AATAGTCGAGAGATCATTTTATAACTTTT
560448 AATA
1 AATA
560452 CTCAGAGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (29 bp):
AATAGTCGAGAGATCATTTTATAACTTTT
Found at i:560895 original size:38 final size:38
Alignment explanation
Indices: 560849--560922 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
560839 CTATCTACAA
*
560849 TCCTAAAAAATCTCTAACCTCATAGTCCATTATTGTCG
1 TCCTAAAAAATCTCTAACCTCAAAGTCCATTATTGTCG
*
560887 TCCTAAAAAATCTCTATCCTCAAAGTCCATTATTGT
1 TCCTAAAAAATCTCTAACCTCAAAGTCCATTATTGT
560923 TGCCGATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (38 bp):
TCCTAAAAAATCTCTAACCTCAAAGTCCATTATTGTCG
Found at i:563495 original size:20 final size:20
Alignment explanation
Indices: 563470--563507 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
563460 TTTATTTTTA
*
563470 AACTTTATTTTAATTATCAT
1 AACTTTATTTCAATTATCAT
*
563490 AACTTTGTTTCAATTATC
1 AACTTTATTTCAATTATC
563508 GAACTTGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.53
Consensus pattern (20 bp):
AACTTTATTTCAATTATCAT
Found at i:563557 original size:33 final size:32
Alignment explanation
Indices: 563497--563610 Score: 169
Period size: 32 Copynumber: 3.6 Consensus size: 32
563487 CATAACTTTG
563497 TTTCAA-TTATCGAACTTGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGAAGTTTTTAAGTA
*
563528 TTTGAATTTATCGAACTTGAAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTG-AAGTTTTTAAGTA
* *
563561 TTTTAATTTATCGAACTTGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGAAGTTTTTAAGTA
563593 TTTCAA-TTATCGTAACTT
1 TTTCAATTTATCG-AACTT
563611 TGTTGCAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 11 0.14
32 34 0.45
33 31 0.41
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.46
Consensus pattern (32 bp):
TTTCAATTTATCGAACTTGAAGTTTTTAAGTA
Found at i:569726 original size:14 final size:14
Alignment explanation
Indices: 569709--569759 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
569699 TATTTTTAAT
*
569709 AAAATGATAATAAA
1 AAAATTATAATAAA
* *
569723 AAAATTATATTACA
1 AAAATTATAATAAA
569737 AAAATTATTAATAAA
1 AAAATTA-TAATAAA
569752 ATAAATTA
1 A-AAATTA
569760 GAGTGATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 6 0.20
16 6 0.20
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AAAATTATAATAAA
Found at i:572827 original size:27 final size:27
Alignment explanation
Indices: 572792--572849 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
572782 ATAAATAACT
572792 ATTATAATGAAATTTAATTTATATCAA
1 ATTATAATGAAATTTAATTTATATCAA
*
572819 ATTATAATGATATTTAATTTATATCAA
1 ATTATAATGAAATTTAATTTATATCAA
572846 ATTA
1 ATTA
572850 AATTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (27 bp):
ATTATAATGAAATTTAATTTATATCAA
Found at i:573227 original size:30 final size:31
Alignment explanation
Indices: 573158--573233 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
573148 GGCAAAATTG
* *
573158 AAAGTTCAGTGGTATAAACGATACAACGTCT
1 AAAGTTTAGTGGTATAAACGATACAACATCT
*
573189 AAATTTTAGTGGTATAAACGATA-AACATCT
1 AAAGTTTAGTGGTATAAACGATACAACATCT
573219 AAAGTTTAGTGGTAT
1 AAAGTTTAGTGGTAT
573234 CTGATTTAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 20 0.49
31 21 0.51
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (31 bp):
AAAGTTTAGTGGTATAAACGATACAACATCT
Found at i:573920 original size:117 final size:113
Alignment explanation
Indices: 573679--573933 Score: 287
Period size: 114 Copynumber: 2.2 Consensus size: 113
573669 GAAAGATATA
* * * *
573679 GACGATAAACATCACAAGAAA-AGTGATCCTAAGCAGAAAGAAGAAGGGCTAATGGGTATGCCCA
1 GACGATAAACATCA-AAGAAAGA-TGATCATAAGCACAAAGAAGAAGGGATAATGGGTATGCCAA
* * *
573743 AAGATAAATTCCATGGTGATGATGAGGATCGTGATCGTAAACATAAAAAC
64 AAAACAAATTCCACGGTGATGATGAGGATCGTGATCGTAAACATAAAAAC
* * * *
573793 GATGATAAACAACATAAGAAAGATGATCATAAGCACAAGGAAGAAGGGATAATGGGTATGTCAAA
1 GACGATAAACATCA-AAGAAAGATGATCATAAGCACAAAGAAGAAGGGATAATGGGTATGCCAAA
* * * **
573858 AAACAAATTTCACGGTGACGATGATGATGATCGTGATCGTAAAGATAAAGGC
65 AAACAAATTCCACGGT---GATGATGAGGATCGTGATCGTAAACATAAAAAC
*
573910 GGCGATAAACATCAAATGAAAGAT
1 GACGATAAACATCAAA-GAAAGAT
573934 AAATACAATA
Statistics
Matches: 116, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
114 66 0.57
115 1 0.01
116 2 0.02
117 47 0.41
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (113 bp):
GACGATAAACATCAAAGAAAGATGATCATAAGCACAAAGAAGAAGGGATAATGGGTATGCCAAAA
AACAAATTCCACGGTGATGATGAGGATCGTGATCGTAAACATAAAAAC
Found at i:575651 original size:3 final size:3
Alignment explanation
Indices: 575638--575694 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
575628 ATTAGTAAAA
575638 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
575685 AAT AAT AAT A
1 AAT AAT AAT A
575695 CAAAACAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:575821 original size:31 final size:30
Alignment explanation
Indices: 575772--575830 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
575762 TTATTACAAG
* * *
575772 TGATGACCGAAATGAATTATACATGAAAATA
1 TGATGACCAAAATAAATTACACAT-AAAATA
*
575803 TGATGACTAAAATAAATTACACATAAAA
1 TGATGACCAAAATAAATTACACATAAAA
575831 GTAAAAGGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (30 bp):
TGATGACCAAAATAAATTACACATAAAATA
Found at i:582825 original size:2 final size:2
Alignment explanation
Indices: 582818--582850 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
582808 TCTCACCCCA
582818 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 A
582851 GAATTATATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:582880 original size:67 final size:67
Alignment explanation
Indices: 582765--582902 Score: 215
Period size: 67 Copynumber: 2.1 Consensus size: 67
582755 GACCGTCGCA
* * *
582765 ATATATATATATATATATAATTATATATCTCAACGACGATATGTCTCACCCCAATATATATATAT
1 ATATATATATATATATATAAATATATATCTCAACGACGATATGCCTCACCACAATATATATATAT
582830 AT
66 AT
* *
582832 ATATATATATATATATATAGAAT-TATATCTCAACGACTATGTGCCTCACCACAATATATATATA
1 ATATATATATATATATATA-AATATATATCTCAACGACGATATGCCTCACCACAATATATATATA
582896 TAT
65 TAT
582899 ATAT
1 ATAT
582903 CAACGACTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 63 0.97
68 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.38
Consensus pattern (67 bp):
ATATATATATATATATATAAATATATATCTCAACGACGATATGCCTCACCACAATATATATATAT
AT
Found at i:582906 original size:41 final size:43
Alignment explanation
Indices: 582840--582968 Score: 172
Period size: 41 Copynumber: 3.0 Consensus size: 43
582830 ATATATATAT
* *
582840 ATATATATATAGAATTATATCTCAACGACTATGTGCCTCACCAC-
1 ATATATATATA-TA-TATATATCAACGACTATGTGCCTCACCACA
* *
582884 A-ATATATATATATATATATCAACGACTATATACCTCACCACA
1 ATATATATATATATATATATCAACGACTATGTGCCTCACCACA
582926 ATATATATATATATATATATCTCAACGACTATGTGCCTCACCA
1 ATATATATATATATATATA--TCAACGACTATGTGCCTCACCA
582969 ACCGCATAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
41 26 0.35
42 2 0.03
43 26 0.35
44 1 0.01
45 20 0.27
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.33
Consensus pattern (43 bp):
ATATATATATATATATATATCAACGACTATGTGCCTCACCACA
Found at i:582934 original size:45 final size:44
Alignment explanation
Indices: 582838--582968 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 44
582828 ATATATATAT
*
582838 ATATATATATATAGAATTATATCTCAACGACTATGTGCCTCACCAC
1 ATATATATATATA-TA-TATATCTCAACGACTATGTGCCTCACCAC
* *
582884 A-ATATATATATATATATA--TCAACGACTATATACCTCACCAC
1 ATATATATATATATATATATCTCAACGACTATGTGCCTCACCAC
582925 AATATATATATATATATATATCTCAACGACTATGTGCCTCACCA
1 -ATATATATATATATATATATCTCAACGACTATGTGCCTCACCA
582969 ACCGCATAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
41 21 0.28
42 1 0.01
43 21 0.28
44 1 0.01
45 31 0.41
46 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (44 bp):
ATATATATATATATATATATCTCAACGACTATGTGCCTCACCAC
Found at i:588165 original size:40 final size:41
Alignment explanation
Indices: 588098--588444 Score: 325
Period size: 41 Copynumber: 8.5 Consensus size: 41
588088 TGATTGAATT
* * *
588098 GAATTGTGAATTATTGAATGATGCCATGATCGAATTAAGTC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
*
588139 GAATTGTGAA-TATTGCATGCTTCCATGATCTAATTAAGTC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
* * *
588179 GAA-TGTGAATTATTGCATGCTTTCATGATCGAATTCAGTT
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
* *
588219 GAATTGTAAATTATTGCATG-TTGCCATGATCGAATTAAGTT
1 GAATTGTGAATTATTGCATGCTT-CCATGATCGAATTAAGTC
* * * * *
588260 GAATTGTGAATTA-TACATGATGCCATAATTGAATTGAA-TC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAATT-AAGTC
* * *
588300 GAATTGTGTATTATTGCATTCTAT-CATGATTGAATTGAA-T-
1 GAATTGTGAATTATTGCATGCT-TCCATGATCGAATT-AAGTC
* * * *
588340 GTAATTGTGAATTATTGAATGTTTCCATGATCAAATTGAGTC
1 G-AATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
* * * * *
588382 GAATGGTGAATTATTGCACGTTTCCATGATTGAACTGAA-TC
1 GAATTGTGAATTATTGCATGCTTCCATGATCGAA-TTAAGTC
* *
588423 GAATTTTGAATTAGTGCATGCT
1 GAATTGTGAATTATTGCATGCT
588445 GCAAAGATCG
Statistics
Matches: 252, Mismatches: 42, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
39 6 0.02
40 92 0.37
41 151 0.60
42 3 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (41 bp):
GAATTGTGAATTATTGCATGCTTCCATGATCGAATTAAGTC
Found at i:588294 original size:81 final size:82
Alignment explanation
Indices: 588096--588411 Score: 310
Period size: 81 Copynumber: 3.9 Consensus size: 82
588086 CATGATTGAA
588096 TTGAATTGTGAATTATTGA-ATGATGCCATGATCGAATTAAGTCGAATTGTGAA-TATTGCATGC
1 TTGAATTGTGAATTATT-ACATGATGCCATGATCGAATTAAGTCGAATTGTGAATTATTGCATGC
*
588159 TTCCATGATCTAATTAAG
65 TTCCATGATCGAATTAAG
* * * ** * * *
588177 TCGAA-TGTGAATTATTGCATGCTTTCATGATCGAATTCAGTTGAATTGTAAATTATTGCATG-T
1 TTGAATTGTGAATTATTACATGATGCCATGATCGAATTAAGTCGAATTGTGAATTATTGCATGCT
588240 TGCCATGATCGAATTAAG
66 T-CCATGATCGAATTAAG
* * * *
588258 TTGAATTGTGAATTA-TACATGATGCCATAATTGAATTGAA-TCGAATTGTGTATTATTGCATTC
1 TTGAATTGTGAATTATTACATGATGCCATGATCGAATT-AAGTCGAATTGTGAATTATTGCATGC
*
588321 TAT-CATGATTGAATTGAA-
65 T-TCCATGATCGAATT-AAG
* * * * * *
588339 -TGTAATTGTGAATTATTGA-ATGTTTCCATGATCAAATTGAGTCGAATGGTGAATTATTGCACG
1 TTG-AATTGTGAATTATT-ACATGATGCCATGATCGAATTAAGTCGAATTGTGAATTATTGCATG
*
588402 TTTCCATGAT
64 CTTCCATGAT
588412 TGAACTGAAT
Statistics
Matches: 189, Mismatches: 33, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
80 43 0.23
81 91 0.48
82 53 0.28
83 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (82 bp):
TTGAATTGTGAATTATTACATGATGCCATGATCGAATTAAGTCGAATTGTGAATTATTGCATGCT
TCCATGATCGAATTAAG
Found at i:589162 original size:20 final size:21
Alignment explanation
Indices: 589137--589175 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
589127 TGTTGTATAT
589137 AGTCGTTGGGGATG-TTTTGG
1 AGTCGTTGGGGATGATTTTGG
*
589157 AGTCGTTTGGGATGATTTT
1 AGTCGTTGGGGATGATTTT
589176 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.13, C:0.05, G:0.38, T:0.44
Consensus pattern (21 bp):
AGTCGTTGGGGATGATTTTGG
Found at i:589262 original size:36 final size:36
Alignment explanation
Indices: 589215--589288 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
589205 TGCATCGGTG
589215 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
1 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
589251 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
1 CACTATCATGGTGCATCGATACCCCTTCATTAAATT
589287 CA
1 CA
589289 AATAAACTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (36 bp):
CACTATCATGGTGCATCGATACCCCTTCATTAAATT
Found at i:589336 original size:12 final size:12
Alignment explanation
Indices: 589319--589378 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 12
589309 CTTGATGCAT
589319 GGATGCATGGCA
1 GGATGCATGGCA
589331 GGATGCAT--C-
1 GGATGCATGGCA
589340 -GATGCATGGCA
1 GGATGCATGGCA
589351 GGATGCAT--C-
1 GGATGCATGGCA
589360 -GATGCATGGCA
1 GGATGCATGGCA
589371 GGATGCAT
1 GGATGCAT
589379 CGATGCATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
8 14 0.35
10 4 0.10
12 22 0.55
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.20
Consensus pattern (12 bp):
GGATGCATGGCA
Found at i:589427 original size:20 final size:20
Alignment explanation
Indices: 589312--589426 Score: 167
Period size: 20 Copynumber: 5.7 Consensus size: 20
589302 TTGCAGCCTT
*
589312 GATGCATGGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
589332 GATGCATCGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
589352 GATGCATCGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
**
589372 GATGCATCGATGCATGGCCTT
1 GATGCATCGATGCATGG-CAG
** *
589393 GATGCATCGATGCACAGAAG
1 GATGCATCGATGCATGGCAG
589413 GATGCATCGATGCA
1 GATGCATCGATGCA
589427 CTAATTGCAT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 70 0.81
21 16 0.19
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:589614 original size:29 final size:29
Alignment explanation
Indices: 589593--589650 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
589583 AAACTTTGAA
589593 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
589622 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
589651 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:589640 original size:30 final size:30
Alignment explanation
Indices: 589593--589652 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
589583 AAACTTTGAA
589593 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
589622 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
589653 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:589787 original size:21 final size:21
Alignment explanation
Indices: 589763--589802 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
589753 ATGTTTAATG
*
589763 AAAAAGATATCAATTGTTAAC
1 AAAAAGATAACAATTGTTAAC
*
589784 AAAATGATAACAATTGTTA
1 AAAAAGATAACAATTGTTA
589803 CCAATTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATAACAATTGTTAAC
Found at i:590994 original size:19 final size:20
Alignment explanation
Indices: 590947--590994 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
590937 TCTAAATCCT
*
590947 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* * *
590967 CTTTAAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
590986 TTTTCAAAA
1 TTTTCAAAA
590995 GAAAATCGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:597580 original size:20 final size:22
Alignment explanation
Indices: 597555--597594 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
597545 TGTTGTATAT
597555 AGTCG-TTGGGGATG-TTTTGG
1 AGTCGTTTGGGGATGATTTTGG
597575 AGTCGTTTGGGGATGATTTT
1 AGTCGTTTGGGGATGATTTT
597595 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.42
Consensus pattern (22 bp):
AGTCGTTTGGGGATGATTTTGG
Found at i:597709 original size:20 final size:20
Alignment explanation
Indices: 597684--597758 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
597674 TTGCAACCTT
*
597684 GATGCATGGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
**
597704 GATGCATCGATGCATGGCCTT
1 GATGCATCGATGCATGG-CAG
* **
597725 GATGCATAGATGCA-CACAAG
1 GATGCATCGATGCATGGC-AG
597745 GATGCATCGATGCA
1 GATGCATCGATGCA
597759 CTAATTGCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 29 0.66
21 14 0.32
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:597737 original size:41 final size:41
Alignment explanation
Indices: 597680--597758 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
597670 GCCGTTGCAA
* **
597680 CCTTGATGCATGGATGCATGGC-AGGATGCATCGATGCATGG
1 CCTTGATGCATAGATGCA-CACAAGGATGCATCGATGCATGG
597721 CCTTGATGCATAGATGCACACAAGGATGCATCGATGCA
1 CCTTGATGCATAGATGCACACAAGGATGCATCGATGCA
597759 CTAATTGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (41 bp):
CCTTGATGCATAGATGCACACAAGGATGCATCGATGCATGG
Found at i:597804 original size:12 final size:13
Alignment explanation
Indices: 597781--597868 Score: 55
Period size: 13 Copynumber: 6.9 Consensus size: 13
597771 GGTGTTTGAG
597781 TGCATGGATGCAC
1 TGCATGGATGCAC
597794 TGCAT-GATGCATC
1 TGCATGGATGCA-C
* *
597807 GATGCACTAG-TGCAGG
1 --TGCA-TGGATGCA-C
597823 TGCATGGATGCAC
1 TGCATGGATGCAC
597836 TGCA-GG--G-A-
1 TGCATGGATGCAC
597844 TGCATGGATGCAC
1 TGCATGGATGCAC
*
597857 TGCAGGGATGCA
1 TGCATGGATGCA
597869 GGGATGCACT
Statistics
Matches: 59, Mismatches: 5, Indels: 22
0.69 0.06 0.26
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 1 0.02
11 1 0.02
12 9 0.15
13 23 0.39
14 8 0.14
15 4 0.07
16 5 0.08
17 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (13 bp):
TGCATGGATGCAC
Found at i:597849 original size:21 final size:20
Alignment explanation
Indices: 597781--597878 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 20
597771 GGTGTTTGAG
*
597781 TGCATGGATGCACTGCATGA
1 TGCATGGATGCACTGCAGGA
*
597801 TGCATCGATGCACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
597823 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
597844 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
597865 TGCAGGGATGCACT
1 TGCATGGATGCACT
597879 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 34 0.49
22 12 0.17
23 5 0.07
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.21
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:597991 original size:29 final size:31
Alignment explanation
Indices: 597959--598018 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
597949 AAAACTTTGA
597959 ATAAATTCAATT-AAGTCCAAAAA-CATTTT
1 ATAAATTCAATTCAAGTCCAAAAACCATTTT
597988 ATAAATTCAATTCAAGTCCAAAAACCATTTT
1 ATAAATTCAATTCAAGTCCAAAAACCATTTT
598019 GCCTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.41
30 11 0.38
31 6 0.21
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (31 bp):
ATAAATTCAATTCAAGTCCAAAAACCATTTT
Found at i:598341 original size:31 final size:31
Alignment explanation
Indices: 598306--598369 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
598296 TGTATATGCA
*
598306 TGAATTG-TTCAAATCGAATTGCTATATAGAT
1 TGAATTGCTT-AAATCGAAATGCTATATAGAT
* *
598337 TGAATTGCTTAATTCGAAATGCTATGTAGAT
1 TGAATTGCTTAAATCGAAATGCTATATAGAT
598368 TG
1 TG
598370 TGTGTTGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (31 bp):
TGAATTGCTTAAATCGAAATGCTATATAGAT
Found at i:608735 original size:33 final size:33
Alignment explanation
Indices: 608673--608735 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
608663 TATTTTTATT
* **
608673 AATTAAATATCTAAATTTAAAATTTATATACCG
1 AATTAAATATCTAAAATTAAAATAAATATACCG
608706 AATTAAATATCTAATAATT-AAATAAATATA
1 AATTAAATATCTAA-AATTAAAATAAATATA
608736 AATTAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (33 bp):
AATTAAATATCTAAAATTAAAATAAATATACCG
Found at i:609162 original size:21 final size:22
Alignment explanation
Indices: 609118--609162 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
609108 TTTTACTTTG
*
609118 AAACTACTAAAATAACTTTTCA
1 AAACTACTAAAATAACTTTACA
* *
609140 AAACTATTAAATTAA-TTTACA
1 AAACTACTAAAATAACTTTACA
609161 AA
1 AA
609163 TTATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (22 bp):
AAACTACTAAAATAACTTTACA
Found at i:617564 original size:31 final size:30
Alignment explanation
Indices: 617529--617601 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
617519 ACATTTATAG
*
617529 TTTAGAGGATAAAACATTCTAAAAACAATAA
1 TTTAGAGGATAAAACATTCCAAAAA-AATAA
* * *
617560 TTTAG-GGACAAAATATTCCGAAAAAATAA
1 TTTAGAGGATAAAACATTCCAAAAAAATAA
*
617589 TATAGAGGATAAA
1 TTTAGAGGATAAA
617602 TGAGTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 9 0.26
30 21 0.60
31 5 0.14
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (30 bp):
TTTAGAGGATAAAACATTCCAAAAAAATAA
Found at i:617626 original size:2 final size:2
Alignment explanation
Indices: 617619--617654 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
617609 TTAAGCCTTA
617619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
617655 CAATCTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:620187 original size:21 final size:20
Alignment explanation
Indices: 620120--620258 Score: 82
Period size: 21 Copynumber: 6.8 Consensus size: 20
620110 AAATGACCAA
***
620120 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
620140 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
620160 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
620181 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
620202 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
620222 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
620243 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
620259 ACACATAAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.01
20 42 0.47
21 47 0.52
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:620287 original size:20 final size:20
Alignment explanation
Indices: 620225--620418 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
620215 CGATTTTCCA
* ** *
620225 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
620245 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
620265 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
620285 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
620305 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
620325 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
620345 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
620365 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
620385 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
620406 AAATCGCAACGCG
1 AAATCGCAACGCG
620419 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:620309 original size:60 final size:60
Alignment explanation
Indices: 620225--620418 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
620215 CGATTTTCCA
* ** * *
620225 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
620285 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
620345 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
620406 AAATCGCAACGCG
1 AAATCGCAACGCG
620419 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:620853 original size:32 final size:33
Alignment explanation
Indices: 620800--620869 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
620790 TTCACTTAGA
* *
620800 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
620833 TTTCATTTCGCG-TGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
620865 TTTCA
1 TTTCA
620870 AGTTAGTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.47
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:620992 original size:20 final size:20
Alignment explanation
Indices: 620948--621057 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
620938 TGCAGAAGAG
*
620948 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
620969 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
620989 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
621010 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
621024 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
621043 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
621058 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:621005 original size:41 final size:38
Alignment explanation
Indices: 620941--621057 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
620931 TTCAATTTGC
* *
620941 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
620979 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
621020 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
621053 AGAAT
1 AGAAT
621058 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:621027 original size:14 final size:14
Alignment explanation
Indices: 621008--621064 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
620998 GAGAAATGAA
621008 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
621022 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
621041 AATCGCAACGAGAG
1 AATCGCAACGAGAG
621055 AATCGCAACG
1 AATCGCAACG
621065 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:621040 original size:33 final size:33
Alignment explanation
Indices: 621000--621080 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
620990 CGCAACGAGA
621000 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
621033 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
621066 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
621081 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:621098 original size:19 final size:19
Alignment explanation
Indices: 621076--621173 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
621066 GAAACCAAAA
*
621076 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
621095 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
*
621109 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
621128 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
621142 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
621161 TCGCGTTGCGATT
1 TCGCGTTGCGATT
621174 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:621117 original size:14 final size:14
Alignment explanation
Indices: 621098--621187 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
621088 TTTCATTTCG
621098 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
621112 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
621131 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
621145 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-T-ATCT
*
621162 CGCGTTGCGATTCTCT
1 --CGTTGCGATTATCT
621178 CGTTGCGATT
1 CGTTGCGATT
621188 TTCATTTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 28 0.46
15 1 0.02
16 6 0.10
17 7 0.11
18 1 0.02
19 18 0.30
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:621123 original size:33 final size:33
Alignment explanation
Indices: 621081--621195 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
621071 CAAAATCGCA
*
621081 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
621114 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
621147 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
621180 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
621196 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:622483 original size:19 final size:20
Alignment explanation
Indices: 622443--622493 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
622433 AACGCGATCC
622443 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
622463 CCAGAATCGCAAATC-GTTT
1 CCAGAATCGCAAATCAGTTT
*
622482 CCAAAATCGCAA
1 CCAGAATCGCAA
622494 CGCGATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:622510 original size:21 final size:20
Alignment explanation
Indices: 622484--622580 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
622474 AATCGTTTCC
622484 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
622505 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
622524 AAAATTCGCATTGCGATTTTCC
1 AAAA-TCGCAACGCGATTTT-G
* * *
622546 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
622566 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
622581 ACACATAAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
19 4 0.07
20 26 0.45
21 25 0.43
22 3 0.05
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:622642 original size:20 final size:20
Alignment explanation
Indices: 622548--622732 Score: 172
Period size: 20 Copynumber: 9.6 Consensus size: 20
622538 GATTTTCCAT
* ** *
622548 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
622568 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
622588 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
622608 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
622628 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
622648 AATCGCAATGCGTATCCG-A
1 AATCGCAACGCGTATCCGTA
*
622667 TATCGCAA--CGTATCCGT-
1 AATCGCAACGCGTATCCGTA
* *
622684 AATCGCAACG-ATAAT---AA
1 AATCGCAACGCGT-ATCCGTA
622701 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
622721 AATCGCAACGCG
1 AATCGCAACGCG
622733 ATATTTAAAG
Statistics
Matches: 134, Mismatches: 20, Indels: 22
0.76 0.11 0.12
Matches are distributed among these distances:
17 27 0.20
18 2 0.01
19 11 0.08
20 92 0.69
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:623171 original size:32 final size:32
Alignment explanation
Indices: 623109--623178 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
623099 TTCACTTAGA
623109 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTGTC-TTGCGAT
* *
623142 TTTCATTTCGCGTTGCTATTCTCGT-TTGCGAT
1 TTTCATTTCGCGTTACGATTCT-GTCTTGCGAT
623174 TTTCA
1 TTTCA
623179 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 12 0.35
33 20 0.59
34 2 0.06
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (32 bp):
TTTCATTTCGCGTTACGATTCTGTCTTGCGAT
Found at i:623314 original size:41 final size:41
Alignment explanation
Indices: 623256--623333 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
623246 TTACAGAAGA
*
623256 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
623297 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
623334 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:623330 original size:21 final size:21
Alignment explanation
Indices: 623257--623332 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
623247 TACAGAAGAG
*
623257 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
623278 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
623298 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
623319 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
623333 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:623374 original size:19 final size:18
Alignment explanation
Indices: 623352--623415 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
623342 GAAACCAAAA
623352 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
* *
623371 TCGCGTGCGA--TTC-TC
1 TCGCTTGCGATTTTCATT
623386 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
623403 TCGCGTTGCGATT
1 TCGC-TTGCGATT
623416 CTCTCGTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 6 0.17
17 4 0.11
18 5 0.14
19 12 0.33
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:623418 original size:33 final size:33
Alignment explanation
Indices: 623357--623469 Score: 160
Period size: 32 Copynumber: 3.5 Consensus size: 33
623347 CAAAATCGCA
623357 TTGCGATTTTCATTTCGCG-TGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
623389 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*** *
623422 TTGCGACAGTCATTCTCTCGTTGCGA-T-TCTCG
1 TTGCGATTTTCATT-TCGCGTTGCGATTCTCTCG
623454 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
623470 AACCAAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 2 0.03
32 35 0.49
33 25 0.35
34 10 0.14
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:623452 original size:14 final size:14
Alignment explanation
Indices: 623376--623427 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
623366 TCATTTCGCG
623376 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
*
623390 TGCGATTTTCATTTCGCGT
1 TGCGA--TTC---TCTCGT
623409 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
623423 TGCGA
1 TGCGA
623428 CAGTCATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 15 0.48
16 3 0.10
17 3 0.10
19 10 0.32
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
TGCGATTCTCTCGT
Found at i:623454 original size:12 final size:12
Alignment explanation
Indices: 623437--623461 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
623427 ACAGTCATTC
623437 TCTCGTTGCGAT
1 TCTCGTTGCGAT
623449 TCTCGTTGCGAT
1 TCTCGTTGCGAT
623461 T
1 T
623462 TTCATTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TCTCGTTGCGAT
Found at i:625478 original size:13 final size:14
Alignment explanation
Indices: 625447--625482 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
625437 TGATTGTTAA
625447 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
625461 ATGATTTGT-AAAG
1 TTGATTTGTAAAAG
625474 TTGATTTGT
1 TTGATTTGT
625483 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:625613 original size:19 final size:19
Alignment explanation
Indices: 625589--625687 Score: 145
Period size: 19 Copynumber: 5.5 Consensus size: 19
625579 AAAATTGACT
625589 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
625608 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
625627 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
625641 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
625660 ATCGCAATGCGGAATGAAA
1 ATCGCAATGCGAAATGAAA
625679 ATCGCAATG
1 ATCGCAATG
625688 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 56 0.78
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:625717 original size:52 final size:52
Alignment explanation
Indices: 625589--625704 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
625579 AAAATTGACT
625589 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
625641 ATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
625693 ATCGCAATGCGA
1 ATCGCAATGCGA
625705 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:625722 original size:19 final size:18
Alignment explanation
Indices: 625694--625823 Score: 77
Period size: 19 Copynumber: 7.7 Consensus size: 18
625684 AATGGGAGAA
*
625694 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTT-ATT
* *
625713 TCGCATTGCGA--TTCTC
1 TCGCATTGCGATTTTATT
625729 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
625746 TCGCATTGCGA--TTCTC
1 TCGCATTGCGATTTTATT
625762 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
625779 TCGCATTGCGA--TTCTC
1 TCGCATTGCGATTTTATT
*
625795 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTTATT
625811 TCGCATTGCGATT
1 TCGCATTGCGATT
625824 CTCTCGTTGC
Statistics
Matches: 83, Mismatches: 14, Indels: 29
0.66 0.11 0.23
Matches are distributed among these distances:
14 18 0.22
16 21 0.25
17 14 0.17
18 8 0.10
19 22 0.27
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:625737 original size:33 final size:33
Alignment explanation
Indices: 625700--625855 Score: 287
Period size: 33 Copynumber: 4.7 Consensus size: 33
625690 AGAATCGCAA
*
625700 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
625733 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
625766 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
625799 TGCGA-TTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
625831 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
625856 AATGTAATGG
Statistics
Matches: 120, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
32 32 0.27
33 78 0.65
34 10 0.08
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:625938 original size:19 final size:19
Alignment explanation
Indices: 625914--626011 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
625904 AAAATTGACT
625914 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
625933 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
625952 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
625966 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
625985 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
626005 ATCGCAA
1 ATCGCAA
626012 CGAGAGATCG
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:626042 original size:52 final size:53
Alignment explanation
Indices: 625914--626029 Score: 218
Period size: 52 Copynumber: 2.2 Consensus size: 53
625904 AAAATTGACT
625914 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
625966 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG-
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
626018 ATCGCAATGCGA
1 ATCGCAATGCGA
626030 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 41 0.65
53 22 0.35
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:628402 original size:24 final size:24
Alignment explanation
Indices: 628368--628414 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
628358 CTGAAACATC
628368 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
628392 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
628415 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:629124 original size:20 final size:20
Alignment explanation
Indices: 629096--629345 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
629086 AAATTTCAGT
* *
629096 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
629116 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
629136 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
629156 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
629176 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
629196 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
629216 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
629236 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * * *
629256 ATTGCGATTTATGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
629276 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
629296 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
629316 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
629336 GTTGCGATTT
1 GTTGCGATTT
629346 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:635010 original size:38 final size:38
Alignment explanation
Indices: 634929--635002 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
634919 AAAAGAGCTT
634929 ATAAACAAGTTTGTTCATGAACATAAACGAATGAGTCA
1 ATAAACAAGTTTGTTCATGAACATAAACGAATGAGTCA
* *
634967 ATAAACACGTTTGTTCCTGAACATAAACGAATGAGT
1 ATAAACAAGTTTGTTCATGAACATAAACGAATGAGT
635003 GGATAAACGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (38 bp):
ATAAACAAGTTTGTTCATGAACATAAACGAATGAGTCA
Found at i:635257 original size:16 final size:16
Alignment explanation
Indices: 635223--635263 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
635213 GTTTACTTCA
* *
635223 GAATGATT-AAGTGCT
1 GAATGATTCAAATCCT
635238 GAATGATTCAAATCCT
1 GAATGATTCAAATCCT
635254 GAATGATTCA
1 GAATGATTCA
635264 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATCCT
Found at i:635368 original size:23 final size:23
Alignment explanation
Indices: 635340--635405 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
635330 TGTACTTTGA
635340 TGCTGAATCATTTAGCACTGTTT
1 TGCTGAATCATTTAGCACTGTTT
635363 TGCTGAATCATTTAGCACTGTTT
1 TGCTGAATCATTTAGCACTGTTT
* * *
635386 TGTTGAATCAGTCAGCACTG
1 TGCTGAATCATTTAGCACTG
635406 AATCATTCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (23 bp):
TGCTGAATCATTTAGCACTGTTT
Found at i:642547 original size:21 final size:19
Alignment explanation
Indices: 642490--642548 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
642480 CTTCCAACAT
*
642490 TAGAGAGTAT-GATACTCAA
1 TAGAAAGTATGGATACTC-A
*
642509 TAGAAAGTATGAATACTCA
1 TAGAAAGTATGGATACTCA
*
642528 TACGAAGAGTTTGGATACTCA
1 TA-GAA-AGTATGGATACTCA
642549 AATAGAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.36
20 9 0.27
21 12 0.36
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (19 bp):
TAGAAAGTATGGATACTCA
Found at i:642557 original size:21 final size:20
Alignment explanation
Indices: 642490--642560 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
642480 CTTCCAACAT
642490 TAGAGAGTAT-GATACTCAA
1 TAGAGAGTATGGATACTCAA
* *
642509 TAGAAAGTATGAATACTC-A
1 TAGAGAGTATGGATACTCAA
*
642528 TACGAAGAGTTTGGATACTCAAA
1 TA-G-AGAGTATGGATACTC-AA
642551 TAGAGAGTAT
1 TAGAGAGTAT
642561 ATATACTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 12 0.29
20 7 0.17
21 18 0.44
22 1 0.02
23 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (20 bp):
TAGAGAGTATGGATACTCAA
Found at i:642614 original size:20 final size:20
Alignment explanation
Indices: 642591--642642 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
642581 CACTTAATGA
642591 TATTGATACCAATCAAAGAG
1 TATTGATACCAATCAAAGAG
642611 TATTGATACCAATCAAAGAG
1 TATTGATACCAATCAAAGAG
642631 TATTGATACCAA
1 TATTGATACCAA
642643 ATTGATGGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.27
Consensus pattern (20 bp):
TATTGATACCAATCAAAGAG
Found at i:646696 original size:26 final size:26
Alignment explanation
Indices: 646660--646715 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
646650 GAGGAGTCGA
* * *
646660 GCTCAGCAATATTTGAGCTCGACTCG
1 GCTCAACAATACTTGAGCTCAACTCG
646686 GCTCAACAATACTTGAGCTCAACTCG
1 GCTCAACAATACTTGAGCTCAACTCG
646712 GCTC
1 GCTC
646716 GTTTACAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (26 bp):
GCTCAACAATACTTGAGCTCAACTCG
Found at i:665653 original size:19 final size:20
Alignment explanation
Indices: 665629--665669 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
665619 TAGCAATTAC
665629 CAAACA-TGCAGCTTCAAAA
1 CAAACACTGCAGCTTCAAAA
*
665648 CAAACATCTTCAGCTTCAAAA
1 CAAACA-CTGCAGCTTCAAAA
665669 C
1 C
665670 CGACCCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
21 13 0.68
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (20 bp):
CAAACACTGCAGCTTCAAAA
Found at i:668608 original size:15 final size:15
Alignment explanation
Indices: 668579--668617 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
668569 TACTTTTTAT
668579 TATTATTTATATTTGA
1 TATT-TTTATATTTGA
*
668595 TATTTTTATGTTTGA
1 TATTTTTATATTTGA
*
668610 TACTTTTA
1 TATTTTTA
668618 AGTATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (15 bp):
TATTTTTATATTTGA
Found at i:672778 original size:17 final size:18
Alignment explanation
Indices: 672756--672796 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
672746 CTACTTGAAA
672756 ATTTTAAAT-TTTTATAT
1 ATTTTAAATATTTTATAT
672773 ATTTTAAATAATTTTATAT
1 ATTTTAAAT-ATTTTATAT
672792 -TTTTA
1 ATTTTA
672797 TTAAAAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 5 0.23
19 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTAAATATTTTATAT
Found at i:675693 original size:25 final size:25
Alignment explanation
Indices: 675662--675761 Score: 200
Period size: 25 Copynumber: 4.0 Consensus size: 25
675652 ATTTAGGGGA
675662 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
675687 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
675712 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
675737 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
675762 GGGTTGATTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:675837 original size:3 final size:3
Alignment explanation
Indices: 675829--675868 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
675819 ATTAATAAAC
675829 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
675869 CGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:675854 original size:22 final size:22
Alignment explanation
Indices: 675821--675864 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
675811 AATATGTAAT
675821 TAATAAACATAATAATAATAAA
1 TAATAAACATAATAATAATAAA
675843 TAATAATA-ATAATAATAATAAA
1 TAATAA-ACATAATAATAATAAA
675865 ATAACGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAACATAATAATAATAAA
Found at i:676174 original size:40 final size:40
Alignment explanation
Indices: 676120--676230 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 40
676110 TATCTAGGGT
*
676120 GACACGGCTCATACGTGATGAAGAGATCTGGTC-GGAGAAA
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCAGCAG-AA
* *
676160 GACACGGCTCATACGTGATGAAGAGATCTGGTCAGCTGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCAGCAGAA
*
676200 GACACGGCTCATACGTGATGAAGAGTTCTGG
1 GACACGGCTCATACGTGATGAAGAGATCTGG
676231 CCATCTAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
40 64 0.97
41 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.21
Consensus pattern (40 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGTCAGCAGAA
Found at i:676305 original size:43 final size:40
Alignment explanation
Indices: 676247--676359 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
676237 AAATGTGATA
* *
676247 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG---TCTAGGGATG
* * * *
676290 ACACGGCTCCTACGTGATGAAGA-GCTCTGGTCTGGGGATG
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCTAGGGATG
*
676330 ACACGGTTCCTACATGATGAGGACGGCTGG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG
676360 CCATCTTTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
40 31 0.53
41 1 0.02
42 1 0.02
43 25 0.43
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (40 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTCTAGGGATG
Found at i:676428 original size:28 final size:28
Alignment explanation
Indices: 676378--676431 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
676368 AGGGTTTATG
* *
676378 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
676406 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
676432 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:676623 original size:66 final size:65
Alignment explanation
Indices: 676447--676629 Score: 215
Period size: 66 Copynumber: 2.8 Consensus size: 65
676437 TTTTAAAAGC
* * *
676447 AACTGTCTCAAAAGAGACCAAATTCGTTTTAAGGGAAACGA-CTCAAAGATGACATTTAAAGGGA
1 AACTGTCTCAAACGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATGACATTTAAAGGGA
*** * * * * * *
676511 AACTGTCTCGTGCAAGACAAAATTCGTTTTTAAGGGAAACGTTCTCAAAGATCGACGTTTCATGG
1 AACTGTCTCAAACGAGACAAAATTC-ATTTTAAGGGAAACGATCTCAAAGAT-GACATTTAAAGG
676576 GA
64 GA
* *
676578 AATTGTCTCAAACGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 AACTGTCTCAAACGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATG
676630 TTTGTTTTGT
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
64 19 0.20
65 15 0.15
66 32 0.33
67 31 0.32
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (65 bp):
AACTGTCTCAAACGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATGACATTTAAAGGGA
Done.