Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005852.1 Hibiscus syriacus cultivar Beakdansim tig00013735_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: 80427
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:862 original size:20 final size:20
Alignment explanation
Indices: 837--890 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
827 TGAAATATGG
*
837 GTGTATCAGTACATACA-AGA
1 GTGTATCGGTACATACATA-A
857 GTGTATCGGTACATACATAA
1 GTGTATCGGTACATACATAA
877 GTGTATCGGTACAT
1 GTGTATCGGTACAT
891 CCCTTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (20 bp):
GTGTATCGGTACATACATAA
Found at i:1454 original size:17 final size:18
Alignment explanation
Indices: 1432--1468 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1422 GCAAAAATTA
1432 ATGAAG-TC-AATATAAAT
1 ATGAAGTTCAAAT-TAAAT
1449 ATGAAGTTCAAATTAAAT
1 ATGAAGTTCAAATTAAAT
1467 AT
1 AT
1469 TCAAACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
ATGAAGTTCAAATTAAAT
Found at i:1867 original size:17 final size:18
Alignment explanation
Indices: 1845--1881 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1835 GCAAAAATTA
1845 ATGAAG-TC-AATATAAAT
1 ATGAAGTTCAAAT-TAAAT
1862 ATGAAGTTCAAATTAAAT
1 ATGAAGTTCAAATTAAAT
1880 AT
1 AT
1882 TCAAACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
ATGAAGTTCAAATTAAAT
Found at i:2205 original size:409 final size:413
Alignment explanation
Indices: 1198--2857 Score: 2887
Period size: 409 Copynumber: 4.0 Consensus size: 413
1188 TCAATTTTGA
1198 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
*
1263 AAGAAGATTTTTAAGAAAATAGCCAATTGTTATAAATAGATATAGATGTAGCTGCTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
*
1328 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGTAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
1393 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
* *
1458 AAATTAAATATTCAAACCATTCAAAAAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACAAACAAATCTAAAAC
*
1523 ATTCAAAATGTTTTAAC-ATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
326 ATTCAAAA--TATTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
1587 TATCCATAGGTGGATCGGGAGGAGG
389 TATCCATAGGTGGATCGGGAGGAGG
* *
1612 AAAATTACTCCCTTACTTTATTATCCCCCTTTTTGTTAAAAC-AAAAGACTCTAGAAAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
*
1676 AAGAAGATTTTTAAGAAAATAGCTAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
*
1741 ATCAAAAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
*
1806 GGTCATATAAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
*
1871 AAATTAAATATTCAAACCATTCATACAAATATATCCAAACATCC-AAAACAAACAAATCTAAAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACAAACAAATCTAAAAC
*
1935 ATTCAAAA-ATTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAACAAGAAAAGGTCTAATTA
326 ATTCAAAATATTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAATTA
1999 TCCATAGGTGGATCGGGA-GAGG
391 TCCATAGGTGGATCGGGAGGAGG
*
2021 AAAATTACTCCTTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAG-AAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
* * *
2085 AAGAAGGTTTTTAAGAAAATAGTCAATTGATATAAATAGATATAGATGTAGCTACTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
2150 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
2215 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
2280 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAAC--AC--ATCTAAAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACAAACAAATCTAAAAC
*
2341 ATTCAAAATGTTTTAACAATAAGTTCAAATTCAATCC---AAAACTAAGCAAGAAAAGGTCTAAT
326 ATTCAAAA--TATTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
2403 TATCCATAGGTGGATCGGGAGGAGG
389 TATCCATAGGTGGATCGGGAGGAGG
2428 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
2493 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
*
2558 ATCAAGAGAAAGATTAGTCATTAGTCTATAACCAATATTCATAAACAATATGTAAATTGGGAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
*
2623 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTA
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
*
2688 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACAAACAAATCTAAAAC
*
2753 ATTCAAAATGTTTTAACATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTATGCAAGAA
326 ATTCAAAA-----T---A----TTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAA
*
2818 AAGGTCTAATTATCCATAGGTGGATCAGGAGGAGG
379 AAGGTCTAATTATCCATAGGTGGATCGGGAGGAGG
2853 AAAAT
1 AAAAT
2858 GTGCTCGCAT
Statistics
Matches: 1187, Mismatches: 34, Indels: 39
0.94 0.03 0.03
Matches are distributed among these distances:
406 61 0.05
407 58 0.05
408 251 0.21
409 314 0.26
410 85 0.07
412 44 0.04
413 254 0.21
414 40 0.03
415 2 0.00
422 25 0.02
425 53 0.04
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (413 bp):
AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACAAACAAATCTAAAAC
ATTCAAAATATTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAATTA
TCCATAGGTGGATCGGGAGGAGG
Found at i:2276 original size:17 final size:18
Alignment explanation
Indices: 2254--2290 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2244 GCAAAAATTA
2254 ATGAAG-TC-AATATAAAT
1 ATGAAGTTCAAAT-TAAAT
2271 ATGAAGTTCAAATTAAAT
1 ATGAAGTTCAAATTAAAT
2289 AT
1 AT
2291 TCAAACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
ATGAAGTTCAAATTAAAT
Found at i:4190 original size:12 final size:13
Alignment explanation
Indices: 4173--4205 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4163 ATGGGAAAAA
*
4173 TTTGAAAACTAT-
1 TTTGAAAACAATG
4185 TTTGAAAACAATG
1 TTTGAAAACAATG
4198 TTTGAAAA
1 TTTGAAAA
4206 ATCATAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:4735 original size:21 final size:21
Alignment explanation
Indices: 4665--4741 Score: 86
Period size: 23 Copynumber: 3.6 Consensus size: 21
4655 AACCCGACGG
* **
4665 GTGTATCGGTACAC-TTGTTA
1 GTGTATCGATACACATTCATA
4685 GTGTATCGATACACATTCA-A
1 GTGTATCGATACACATTCATA
4705 GGAATGTATCGATACACATTCATA
1 -G--TGTATCGATACACATTCATA
4729 GTGTATCGATACA
1 GTGTATCGATACA
4742 TAGCGAGGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 14 0.29
21 15 0.31
23 19 0.39
24 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (21 bp):
GTGTATCGATACACATTCATA
Found at i:20436 original size:32 final size:32
Alignment explanation
Indices: 20390--20462 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
20380 CTACACAACC
*
20390 CAAACAACATATGTATTGGATAACCCTGCCAG
1 CAAACAACAAATGTATTGGATAACCCTGCCAG
20422 CAAACAACAAATGTATTGGATAACCCTGCCAG
1 CAAACAACAAATGTATTGGATAACCCTGCCAG
20454 CAAACAACA
1 CAAACAACA
20463 TATAACATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (32 bp):
CAAACAACAAATGTATTGGATAACCCTGCCAG
Found at i:25302 original size:2 final size:2
Alignment explanation
Indices: 25295--25322 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25285 TATACCCATA
25295 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
25323 GCATATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26176 original size:22 final size:23
Alignment explanation
Indices: 26135--26177 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
26125 TGATCAAACC
* *
26135 TGGGGCAAGGGAAGTCAAATTTT
1 TGGGGCAAGGAAAATCAAATTTT
26158 TGGGGCAAGGAAAAT-AAATT
1 TGGGGCAAGGAAAATCAAATT
26178 GTCTCAGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (23 bp):
TGGGGCAAGGAAAATCAAATTTT
Found at i:26888 original size:102 final size:98
Alignment explanation
Indices: 26742--27142 Score: 275
Period size: 101 Copynumber: 3.9 Consensus size: 98
26732 TAAGACATGA
* *
26742 ACATTTGATATTGTTTTTCCTCAAAACAAACTTTGTCTCTCTTGAGACAGTTTCCTTCTAAAAAC
1 ACATTTGATATTGTTTTT-CTCAAAACAAA-TTTGTCTCGCTTGAGACAATTTCCTTC-AAAAAC
*
26807 AAATCTTGAAATTGTTTCACTTGAAACAAAATTGATG
63 AAAT-TTGAAATTGTTTCACTTGAAACAAAATTGATC
* * * * * ** * *
26844 ACATTTGATATTGTTTTTACTCGAAGCAAATTTCATCTCGCTTGAGATAATTCCCTTGGAACATA
1 ACATTTGATATTGTTTTT-CTCAAAACAAATTT-GTCTCGCTTGAGACAATTTCCTTCAAAAACA
* * * *
26909 AATTTCAAAGTTATTTTACTTGAAACAAAATTAATC
64 AATTTGAAA-TTGTTTCACTTGAAACAAAATTGATC
* * * * *
26945 TCACTTGATATTGTTTCTT-TCAAAACAAATTTTGTCTCGCTAGAAACGATTTTTCC-TCAAAAT
1 ACATTTGATATTGTTT-TTCTCAAAACAAA-TTTGTCTCGCTTGAGAC-A-ATTTCCTTCAAAA-
* *
27008 ACAAAATTTAGAAATTGTTTCACTTGAAACATAATTGAAAC
61 AC-AAATTT-GAAATTGTTTCACTTGAAACAAAATTG-ATC
* ** * * * * *
27049 ACAAATCTTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCTCATGAAA
1 AC--A--TTTGATATTGTTTTTCTCAAAACAAA-TTTGTCTCGCTTGAGACAATTTC-CTTCAAA
* * * *
27114 CATAAACTTTGAGATTGTTTCTCTTGAAA
60 AACAAA-TTTGAAATTGTTTCACTTGAAA
27143 TAAATTTTGT
Statistics
Matches: 229, Mismatches: 52, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
100 23 0.10
101 53 0.23
102 52 0.23
103 25 0.11
104 6 0.03
106 25 0.11
107 8 0.03
108 37 0.16
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (98 bp):
ACATTTGATATTGTTTTTCTCAAAACAAATTTGTCTCGCTTGAGACAATTTCCTTCAAAAACAAA
TTTGAAATTGTTTCACTTGAAACAAAATTGATC
Found at i:27126 original size:65 final size:66
Alignment explanation
Indices: 27042--27312 Score: 384
Period size: 67 Copynumber: 4.1 Consensus size: 66
27032 TGAAACATAA
* * * *
27042 TTGAAACACAAATCTTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCT
1 TTGAAACATAAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
27107 C
66 C
* * * *
27108 ATGAAACAT-AAACTTTGAGATTGTTTCTCTTGAAATAAATTTTGTTTCTCTTGAGACAATTTCT
1 TTGAAACATAAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
27172 C
66 C
* * *
27173 TTGAAACATAAAAACATTGAGAATGTTTCTCTTGAAACAAATTTTGTCTCTCTTTAGACAGTTTC
1 TTGAAACAT-AAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
27238 TC
65 TC
* * *
27240 TTGAAACATAAAAATATTGAGATTGTTTCCCTTGAAACAAATTTT-TCTCTCTTGAGATAGTTTC
1 TTGAAACATAAAACT-TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
27304 TC
65 TC
27306 TTGAAAC
1 TTGAAAC
27313 TTTATCCCTA
Statistics
Matches: 181, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
65 58 0.32
66 37 0.20
67 86 0.48
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (66 bp):
TTGAAACATAAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
C
Found at i:27560 original size:137 final size:137
Alignment explanation
Indices: 27312--27723 Score: 574
Period size: 137 Copynumber: 3.0 Consensus size: 137
27302 TCTCTTGAAA
*
27312 CTTTATCCCTAAAGATGGTCAGACATCCTCATCACGTAGGAATTGTGTCATCCACCGACCAGATC
1 CTTTATCCCTAAAGATGGTCAGACATCCTCATCACGTAGGAATAGTGTCATCCACCGACCAGATC
** *
27377 TCCTCATCACGTAGGAGCAATGTCAACCTTAGATAACCAGACTTCCTCATCATGTAGGAATCGTG
66 TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCGTG
27442 TTATCTC
131 TTATCTC
* * * * **
27449 CTTTATCCTTAAAGATGGTCAGACGTTCTCATCATGTAGGAACCGTGTCATCCACCGACCAGATC
1 CTTTATCCCTAAAGATGGTCAGACATCCTCATCACGTAGGAATAGTGTCATCCACCGACCAGATC
* * * *
27514 TCCTCATCGCGTAGGAGCAGCGTTAACCTTAGATAACCAGAATTCCTCATCGCGTAGGAATCGTG
66 TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCGTG
27579 TTATCTC
131 TTATCTC
* * * * * * *
27586 CATTTATCCCTAAATATGGACAGTCATCCTCATCGCCTAGGAATAGTGTCATCCACTGACTAGAT
1 C-TTTATCCCTAAAGATGGTCAGACATCCTCATCACGTAGGAATAGTGTCATCCACCGACCAGAT
* * * * *
27651 CTCCTCATCACGTAGGA-CCGCGTCACCCTTAGATAACCAGACTTCCTCATCACGTATGAACCAT
65 CTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCGT
27715 GTTATCTC
130 GTTATCTC
27723 C
1 C
27724 AAATTTACCT
Statistics
Matches: 239, Mismatches: 35, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
137 173 0.72
138 66 0.28
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (137 bp):
CTTTATCCCTAAAGATGGTCAGACATCCTCATCACGTAGGAATAGTGTCATCCACCGACCAGATC
TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCGTG
TTATCTC
Found at i:27917 original size:3 final size:3
Alignment explanation
Indices: 27909--27952 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
27899 CGGGTCATAA
*
27909 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
27953 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:28554 original size:17 final size:19
Alignment explanation
Indices: 28519--28556 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28509 ATAGACATAC
28519 AACCAGTTTGAACAGGGGG
1 AACCAGTTTGAACAGGGGG
28538 AACCAGTTT-AA-AGGGGG
1 AACCAGTTTGAACAGGGGG
28555 AA
1 AA
28557 AATGAGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.37, C:0.13, G:0.34, T:0.16
Consensus pattern (19 bp):
AACCAGTTTGAACAGGGGG
Found at i:29622 original size:15 final size:16
Alignment explanation
Indices: 29593--29622 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29583 ATTTCACATA
29593 TTTCCATTCGCATTTG
1 TTTCCATTCGCATTTG
29609 TTTCCATT-GCATTT
1 TTTCCATTCGCATTT
29623 CTTTATCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.23, G:0.10, T:0.53
Consensus pattern (16 bp):
TTTCCATTCGCATTTG
Found at i:34225 original size:30 final size:31
Alignment explanation
Indices: 34152--34225 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
34142 ATTTTTTATC
*
34152 TATGTACCTAAAA-TATTTTTTTTGTCAAAA
1 TATGTACCTAAAATTATTTTTTTGGTCAAAA
* **
34182 TAAGT-GTTGAAAATTA-TTTTTTGGTCAAAA
1 TATGTACCT-AAAATTATTTTTTTGGTCAAAA
34212 TATGTACCTAAAAT
1 TATGTACCTAAAAT
34226 AATTAATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
29 1 0.03
30 30 0.88
31 3 0.09
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (31 bp):
TATGTACCTAAAATTATTTTTTTGGTCAAAA
Found at i:34347 original size:28 final size:26
Alignment explanation
Indices: 34311--34374 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
34301 AAAAAGTTTG
* *
34311 AATAGTTTAGTTACCTATTTTGGCATAA
1 AATATTTTAG-TACCTATTTTAGCA-AA
* *
34339 AATATTTTAAGTACTTATTTTATCAAA
1 AATATTTT-AGTACCTATTTTAGCAAA
34366 AATATTTTA
1 AATATTTTA
34375 AATACTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 10 0.32
28 18 0.58
29 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (26 bp):
AATATTTTAGTACCTATTTTAGCAAA
Found at i:34995 original size:41 final size:41
Alignment explanation
Indices: 34950--35099 Score: 112
Period size: 41 Copynumber: 3.6 Consensus size: 41
34940 GTACTTTAGC
34950 GGCGTTGTTATACAAACGCCGCAATAGGTTTCATATATAGT
1 GGCGTTGTTATACAAACGCCGCAATAGGTTTCATATATAGT
* * * * * *
34991 GGCGTTTATTCA-AAAAACGCCACAACAGAG--T-AGTACTTTAGC
1 GGCG-TTGTT-ATACAAACGCCGCAATAG-GTTTCA-TA-TATAGT
* * ** *
35033 GGCCTTGTTAGACAAACGTTGCGATAGGTTTCATATATAGT
1 GGCGTTGTTATACAAACGCCGCAATAGGTTTCATATATAGT
35074 GGCGTT-TCTATACAAACGCCGCAATA
1 GGCGTTGT-TATACAAACGCCGCAATA
35100 AGATTAATTT
Statistics
Matches: 78, Mismatches: 21, Indels: 20
0.66 0.18 0.17
Matches are distributed among these distances:
40 4 0.05
41 44 0.56
42 27 0.35
43 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
GGCGTTGTTATACAAACGCCGCAATAGGTTTCATATATAGT
Found at i:35023 original size:83 final size:83
Alignment explanation
Indices: 34878--35080 Score: 252
Period size: 83 Copynumber: 2.5 Consensus size: 83
34868 TGGTGTTTTC
* * * * * *
34878 ATACAAACGCCGCTAAT--G-TT-ATAATATTGTGACGTTTTTTCAACAAACGCCGCAAAATAGT
1 ATACAAACGCCGC-AATAGGTTTCAT-ATATAGTGGCGTTTATTCAAAAAACGCCACAAAAGAGT
*
34939 AGTACTTTAGCGGCGTTGTT
64 AGTACTTTAGCGGCCTTGTT
*
34959 ATACAAACGCCGCAATAGGTTTCATATATAGTGGCGTTTATTCAAAAAACGCCACAACAGAGTAG
1 ATACAAACGCCGCAATAGGTTTCATATATAGTGGCGTTTATTCAAAAAACGCCACAAAAGAGTAG
35024 TACTTTAGCGGCCTTGTT
66 TACTTTAGCGGCCTTGTT
* ** *
35042 AGACAAACGTTGCGATAGGTTTCATATATAGTGGCGTTT
1 ATACAAACGCCGCAATAGGTTTCATATATAGTGGCGTTT
35081 CTATACAAAC
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
80 3 0.03
81 13 0.12
82 1 0.01
83 87 0.82
84 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (83 bp):
ATACAAACGCCGCAATAGGTTTCATATATAGTGGCGTTTATTCAAAAAACGCCACAAAAGAGTAG
TACTTTAGCGGCCTTGTT
Found at i:35140 original size:124 final size:123
Alignment explanation
Indices: 34946--35215 Score: 342
Period size: 124 Copynumber: 2.2 Consensus size: 123
34936 AGTAGTACTT
* * * *** *
34946 TAGCGGCGTTGTTATACAAACGCCGCAATAGGTTTCATATATAGTGGCGTTTATTCAAAAAACGC
1 TAGCGGCGTT-TTATACAAACGCCGCAATAAGATTAATATATAGAACCATTTATTCAAAAAACGC
* * *
35011 CACAACAGAGTAGTACTTTAGCGGCCTTGTTAGACAAACGTTGCGATAGGTTTCATATA
65 CACAACAGAGTAGTACTTTAGCGGCCTAGTTAGACAAACGCTGCAATAGGTTTCATATA
* * * *
35070 TAGTGGCGTTTCTATACAAACGCCGCAATAAGATTAATTTATAGAACCATTTTTTCAACAAACGC
1 TAGCGGCGTTT-TATACAAACGCCGCAATAAGATTAATATATAGAACCATTTATTCAAAAAACGC
* * * *
35135 CACAACATAGTAGTACTTTAGCGGCGTAGTTAGACAAACGCTGTAATAGGTTTCATATT
65 CACAACAGAGTAGTACTTTAGCGGCCTAGTTAGACAAACGCTGCAATAGGTTTCATATA
*
35194 TAGCGGCGTTTTTAGACAAACG
1 TAGCGGCG-TTTTATACAAACG
35216 ACGCTATTCC
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
123 1 0.01
124 120 0.97
125 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (123 bp):
TAGCGGCGTTTTATACAAACGCCGCAATAAGATTAATATATAGAACCATTTATTCAAAAAACGCC
ACAACAGAGTAGTACTTTAGCGGCCTAGTTAGACAAACGCTGCAATAGGTTTCATATA
Found at i:35245 original size:124 final size:121
Alignment explanation
Indices: 34990--35248 Score: 284
Period size: 124 Copynumber: 2.1 Consensus size: 121
34980 TCATATATAG
* * * *
34990 TGGCGTTTATTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCCTTGTTAGACAAACGTTGC
1 TGGCATTTTTTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCCTAGTTAGACAAACGCTGC
* * * * * *
35055 GATAGGTTTCATATATAGTGGCGTTTCTATACAAACGCCGCAATAAGATTAATTTA
66 AATAGGTTTCATATATAGCGGCGTTTCTAGACAAACGACGCAATAACATTAATTAA
* * * *
35111 TAGAACCATTTTTTCAACAAACGCCACAACATAGTAGTACTTTAGCGGCGTAGTTAGACAAACGC
1 T-G--GCATTTTTTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCCTAGTTAGACAAACGC
* * * * **
35176 TGTAATAGGTTTCATATTTAGCGGCGTTTTTAGACAAACGACGCTATTCCCATGTAATGTAA
63 TGCAATAGGTTTCATATATAGCGGCGTTTCTAGACAAACGACGC-AATAACAT-TAAT-TAA
35238 TGGCATTTTTT
1 TGGCATTTTTT
35249 GTAATAAACG
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
121 1 0.01
122 1 0.01
124 97 0.87
125 4 0.04
126 5 0.05
127 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (121 bp):
TGGCATTTTTTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCCTAGTTAGACAAACGCTGC
AATAGGTTTCATATATAGCGGCGTTTCTAGACAAACGACGCAATAACATTAATTAA
Found at i:35273 original size:43 final size:42
Alignment explanation
Indices: 35226--35316 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
35216 ACGCTATTCC
35226 CATGTAATGTAATGGCATTTTT-TGTAATAAACGCCGCAATAGT
1 CATGTAATGTAATGGCATTTTTAT-T-ATAAACGCCGCAATAGT
* * * * *
35269 CATGTACTTTAGTGGTATTTTTATTATAAATGCCGCAATAGT
1 CATGTAATGTAATGGCATTTTTATTATAAACGCCGCAATAGT
35311 CATGTA
1 CATGTA
35317 TGCTTCCTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 22 0.52
43 19 0.45
44 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (42 bp):
CATGTAATGTAATGGCATTTTTATTATAAACGCCGCAATAGT
Found at i:35821 original size:61 final size:61
Alignment explanation
Indices: 35726--35849 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
35716 CTCCTGTCGG
35726 AGCCCTAATTTCTTCATCACTATTGATCCTCCATCAGTTCTCTACGCTCAATATCATCTTC
1 AGCCCTAATTTCTTCATCACTATTGATCCTCCATCAGTTCTCTACGCTCAATATCATCTTC
35787 AGCCCTAATTTCTTCATCACTATTGATCCTCCATCAGTTCTCTACGCTCAATATCATCTTC
1 AGCCCTAATTTCTTCATCACTATTGATCCTCCATCAGTTCTCTACGCTCAATATCATCTTC
35848 AG
1 AG
35850 TAAATCGGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.23, C:0.32, G:0.07, T:0.37
Consensus pattern (61 bp):
AGCCCTAATTTCTTCATCACTATTGATCCTCCATCAGTTCTCTACGCTCAATATCATCTTC
Found at i:37413 original size:12 final size:12
Alignment explanation
Indices: 37395--37423 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
37385 CTTATGAACA
37395 CTTTTTTTTT-T
1 CTTTTTTTTTCT
37406 CTTTTTTTTTCT
1 CTTTTTTTTTCT
37418 CTTTTT
1 CTTTTT
37424 AGATTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
CTTTTTTTTTCT
Found at i:60221 original size:21 final size:21
Alignment explanation
Indices: 60197--60241 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
60187 GAAATGTCAT
*
60197 ATATTTATCCCGGAGGACCAC
1 ATATTTATCCCGAAGGACCAC
*
60218 ATATTTATCCCGAAGGATCAC
1 ATATTTATCCCGAAGGACCAC
60239 ATA
1 ATA
60242 AGACCCTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (21 bp):
ATATTTATCCCGAAGGACCAC
Found at i:61903 original size:20 final size:21
Alignment explanation
Indices: 61878--61917 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
61868 CTCTACATAG
61878 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
61898 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
61918 CCCAACGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:67713 original size:2 final size:2
Alignment explanation
Indices: 67708--67742 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
67698 TGAACACACA
67708 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 A
67743 AATGCTGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68388 original size:3 final size:3
Alignment explanation
Indices: 68374--68431 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
68364 ATTTTTGCCC
* * *
68374 ATT ATC ATT ATT ATT ATT A-T ATT ATT ATT ACT ATT ATT A-T ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
68420 AAT ATT ATT ATT
1 ATT ATT ATT ATT
68432 TTACAAATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:68402 original size:17 final size:17
Alignment explanation
Indices: 68374--68430 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
68364 ATTTTTGCCC
*
68374 ATTATCATTATTATTATT
1 ATTAT-ATTATTAATATT
*
68392 A-TATTATTATTACTATT
1 ATTA-TATTATTAATATT
*
68409 ATTATATAATTAATATT
1 ATTATATTATTAATATT
68426 ATTAT
1 ATTAT
68431 TTTACAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATTATTAATATT
Found at i:68403 original size:20 final size:20
Alignment explanation
Indices: 68374--68431 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
68364 ATTTTTGCCC
*
68374 ATTATCATTATTATTATTAT
1 ATTATTATTATTATTATTAT
*
68394 ATTATTATTACTATTATTAT
1 ATTATTATTATTATTATTAT
* *
68414 ATAATTAATATTATTATT
1 ATTATTATTATTATTATT
68432 TTACAAATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTATTATTATTATTAT
Found at i:68554 original size:16 final size:16
Alignment explanation
Indices: 68533--68580 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
68523 ATCAAATTCA
*
68533 AATCCGGTCCATACCC
1 AATCCGGTCCAGACCC
68549 AATCCGGTCCAGACCC
1 AATCCGGTCCAGACCC
68565 AATCCGGTCCAGACCC
1 AATCCGGTCCAGACCC
68581 GACCCAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.44, G:0.17, T:0.15
Consensus pattern (16 bp):
AATCCGGTCCAGACCC
Found at i:69255 original size:20 final size:20
Alignment explanation
Indices: 69230--69276 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
69220 GGCTTTAGGG
**
69230 TAGTGACCAGCGGTGGTGAA
1 TAGTGACCAGCAATGGTGAA
* *
69250 TAGTGATCGGCAATGGTGAA
1 TAGTGACCAGCAATGGTGAA
69270 TAGTGAC
1 TAGTGAC
69277 AGGAGGTGGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.36, T:0.23
Consensus pattern (20 bp):
TAGTGACCAGCAATGGTGAA
Found at i:75801 original size:5 final size:5
Alignment explanation
Indices: 75791--75988 Score: 120
Period size: 5 Copynumber: 37.8 Consensus size: 5
75781 ATCAGAGAAA
* * *
75791 AAAAG AAAAG AAGAA- AAAAGGG AAAAG -AAGG AAAAA AAAAA AAAAG
1 AAAAG AAAAG AA-AAG AAAA--G AAAAG AAAAG AAAAG AAAAG AAAAG
* *
75837 AAAAA AAAAG AAAA- AAAAA AAAAG AAAAGAG AAAGAG AAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAA-AG AAA-AG AAAAG -AAAAG
* *
75885 AAAAG AAAAG AAAAGAG AAAAG AAAAGAG AAAAG AGAA- AAGAG AAAAG
1 AAAAG AAAAG -AAA-AG AAAAG -AAA-AG AAAAG AAAAG AAAAG AAAAG
* * * *
75933 AGAA- AATAG AAAAG AAAAG AGAAAG AGAAAG AGAA- AAGAG AAAGAG
1 AAAAG AAAAG AAAAG AAAAG A-AAAG A-AAAG AAAAG AAAAG AAA-AG
75979 AAGAAG AAAA
1 AA-AAG AAAA
75989 AATTGAATCA
Statistics
Matches: 155, Mismatches: 19, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
4 15 0.10
5 79 0.51
6 50 0.32
7 11 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:75815 original size:17 final size:16
Alignment explanation
Indices: 75786--75989 Score: 119
Period size: 16 Copynumber: 12.6 Consensus size: 16
75776 TATCCATCAG
75786 AGAAAAAAAGAAAAGA
1 AGAAAAAAAGAAAAGA
*
75802 AGAAAAAAGGGAAAAGA
1 AGAAAAAA-AGAAAAGA
*
75819 AGGAAAAAAA-AAAAAA
1 A-GAAAAAAAGAAAAGA
75835 AGAAAAAAAAAGAAAA-A
1 AG--AAAAAAAGAAAAGA
75852 A-AAAAAAAGAAAAG-
1 AGAAAAAAAGAAAAGA
*
75866 AG--AAAGAGAAAAGA
1 AGAAAAAAAGAAAAGA
75880 A-AAAGAAAAGAAAAGA
1 AGAAA-AAAAGAAAAGA
75896 A-AAGAGAAAAGAAAAG-
1 AGAA-A-AAAAGAAAAGA
*
75912 AG-AAAAGAGAAAAG-
1 AGAAAAAAAGAAAAGA
*
75926 AGAAAAGAGAA-AATAGA
1 AGAAAA-A-AAGAAAAGA
75943 A-AAGAAAAGAGAAAGAGAA
1 AGAA-AAAA-AGAAA-AG-A
*
75962 AGAGAAAAGAGAAAGAGA
1 AGA-AAAAAAGAAA-AGA
75980 AGAAGAAAAA
1 AGAA-AAAAA
75990 ATTGAATCAA
Statistics
Matches: 152, Mismatches: 11, Indels: 48
0.72 0.05 0.23
Matches are distributed among these distances:
13 10 0.07
14 25 0.16
15 7 0.05
16 38 0.25
17 36 0.24
18 21 0.14
19 10 0.07
20 4 0.03
21 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGAAAAGA
Found at i:75826 original size:1 final size:1
Alignment explanation
Indices: 75822--75864 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
75812 GAAAAGAAGG
* * *
75822 AAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
75865 GAGAAAGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:75832 original size:25 final size:24
Alignment explanation
Indices: 75787--75860 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 24
75777 ATCCATCAGA
*
75787 GAAAAAAAGAAAAGAAGAAAAAAGG
1 GAAAAAAAGAAAA-AAAAAAAAAGG
* *
75812 GAAAAGAAGGAAAAAAAAAAAAAAGA
1 GAAAA-AAAG-AAAAAAAAAAAAAGG
*
75838 AAAAAAAAGAAAAAAAAAAAAAG
1 GAAAAAAAGAAAAAAAAAAAAAG
75861 AAAAGAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
24 14 0.33
25 8 0.19
26 16 0.38
27 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
GAAAAAAAGAAAAAAAAAAAAAGG
Found at i:75835 original size:19 final size:18
Alignment explanation
Indices: 75788--75990 Score: 110
Period size: 19 Copynumber: 10.8 Consensus size: 18
75778 TCCATCAGAG
*
75788 AAAAAAAGAAAAGAAG-A
1 AAAAAAAGAAAAAAAGAA
** * *
75805 AAAAAGGGAAAAGAAG-G
1 AAAAAAAGAAAAAAAGAA
75822 AAAAAAA-AAAAAAAGAA
1 AAAAAAAGAAAAAAAGAA
*
75839 AAAAAAAGAAAAAAAAAA
1 AAAAAAAGAAAAAAAGAA
* *
75857 AAAGAAAAGAGAAAGAGAA
1 AAA-AAAAGAAAAAAAGAA
75876 AAGAAAAAGAAAAGAAAAGAA
1 AA-AAAAAG-AAA-AAAAGAA
*
75897 AAGAGAAAAG-AAAAGAGAA
1 AA-A-AAAAGAAAAAAAGAA
*
75916 AAGAGAAAAGAGAAAAGAGAA
1 AA-A-AAAAGA-AAAAAAGAA
*
75937 AATAGAAAAG-AAAAGAGAA
1 AA-A-AAAAGAAAAAAAGAA
* * *
75956 AGAGAAAGAGAAAAGAGAA
1 AAAAAAAGA-AAAAAAGAA
*
75975 AGAGAAGAAGAAAAAA
1 A-A-AAAAAGAAAAAA
75991 TTGAATCAAG
Statistics
Matches: 152, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
16 7 0.05
17 30 0.20
18 13 0.09
19 55 0.36
20 9 0.06
21 33 0.22
22 5 0.03
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAGAA
Found at i:75846 original size:29 final size:28
Alignment explanation
Indices: 75786--75969 Score: 96
Period size: 33 Copynumber: 6.2 Consensus size: 28
75776 TATCCATCAG
*
75786 AGAAAAAAAGAAAAGAAGAAAAAAGGGAAAAGA
1 AGAAAAAAA-AAAAAAAG-AAAAA---AAAAGA
75819 AGGAAAAAAAAAAAAAAG--AAAAAAA-A
1 A-GAAAAAAAAAAAAAAGAAAAAAAAAGA
*
75845 AG-AAAAAAAAAAAAAGAAAAGAGAAAG-
1 AGAAAAAAAAAAAAAAGAAAA-AAAAAGA
* *
75872 AGAAAAGAAAAAGAAAAGAAAAGAAAAG-
1 AGAAAA-AAAAAAAAAAGAAAAAAAAAGA
75900 AGAAAAGAAAAGAGAAAAGAGAAAAGAGAAAAG-
1 AGAAAA-AAAA-A-AAAA-AGAAAA-A-AAAAGA
* *
75933 AGAAAATAGAAAAGAAAAGAGAAAGAGAAAG-
1 AGAAAA-A-AAAA-AAAA-AGAAAAAAAAAGA
75964 AGAAAA
1 AGAAAA
75970 GAGAAAGAGA
Statistics
Matches: 128, Mismatches: 10, Indels: 28
0.77 0.06 0.17
Matches are distributed among these distances:
24 14 0.11
25 1 0.01
26 4 0.03
27 10 0.08
28 18 0.14
29 15 0.12
30 6 0.05
31 16 0.12
32 1 0.01
33 32 0.25
34 11 0.09
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.01
Consensus pattern (28 bp):
AGAAAAAAAAAAAAAAGAAAAAAAAAGA
Found at i:75869 original size:7 final size:7
Alignment explanation
Indices: 75830--75989 Score: 150
Period size: 7 Copynumber: 24.6 Consensus size: 7
75820 GGAAAAAAAA
*
75830 AAAAAAG
1 AAAAGAG
75837 AAAA-A-
1 AAAAGAG
75842 AAAAGA-
1 AAAAGAG
*
75848 AAAA-AA
1 AAAAGAG
*
75854 AAAAAAG
1 AAAAGAG
75861 AAAAGAG
1 AAAAGAG
75868 -AAAGAG
1 AAAAGAG
75874 AAAAGA-
1 AAAAGAG
*
75880 AAAAGAA
1 AAAAGAG
*
75887 AAGAAAAG
1 AA-AAGAG
75895 AAAAGAG
1 AAAAGAG
75902 -AAA-AG
1 AAAAGAG
75907 AAAAGAG
1 AAAAGAG
75914 AAAAGAG
1 AAAAGAG
75921 AAAAGAG
1 AAAAGAG
75928 AAAAGAG
1 AAAAGAG
*
75935 AAAATAG
1 AAAAGAG
75942 -AAA-AG
1 AAAAGAG
75947 AAAAGAG
1 AAAAGAG
75954 -AAAGAG
1 AAAAGAG
75960 -AAAGAG
1 AAAAGAG
75966 AAAAGAG
1 AAAAGAG
75973 -AAAGAG
1 AAAAGAG
75979 AAGAAGA-
1 AA-AAGAG
75986 AAAA
1 AAAA
75990 ATTGAATCAA
Statistics
Matches: 134, Mismatches: 6, Indels: 27
0.80 0.04 0.16
Matches are distributed among these distances:
5 9 0.07
6 54 0.40
7 62 0.46
8 9 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.01
Consensus pattern (7 bp):
AAAAGAG
Found at i:77412 original size:52 final size:51
Alignment explanation
Indices: 77219--77400 Score: 240
Period size: 51 Copynumber: 3.6 Consensus size: 51
77209 AGTCCATATT
* * * *
77219 ATCCATGT-GGGTATCTTGAAGGCTAACTTCAGCATGAAAAGATAGAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTA
* * *
77269 ATCCATGTGGGGCATCTTGAAGGTTCACATAAGCATGAAAAGACAGAATTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTA
* *
77320 ATCCATGTGGGGCATCTTGAAGGCTCACATCTGCATGAAAATGACATAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAA-GACAGAAGTA
* * *
77372 ATCGATGTGGAGAATCTTGAAGGCTCACA
1 ATCCATGTGGGGCATCTTGAAGGCTCACA
77401 CCAGTTTGAA
Statistics
Matches: 115, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 8 0.07
51 73 0.63
52 34 0.30
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (51 bp):
ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTA
Found at i:77971 original size:54 final size:54
Alignment explanation
Indices: 77896--78001 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
77886 TACTGACAAG
*
77896 AAATCTGGGCAGAAGCCACATGAAAGGATGAATGTGTTATCAAATGTTTTACGA
1 AAATCTGGGCAGAAGCCACATGAAAGGATGAATGTGTTATAAAATGTTTTACGA
* *
77950 AAATCTGGGCAGAAGGCACATGAAAGGATGAATGTGTTGTAAAATGTTTTAC
1 AAATCTGGGCAGAAGCCACATGAAAGGATGAATGTGTTATAAAATGTTTTAC
78002 AAACTAGTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.26
Consensus pattern (54 bp):
AAATCTGGGCAGAAGCCACATGAAAGGATGAATGTGTTATAAAATGTTTTACGA
Found at i:79401 original size:177 final size:177
Alignment explanation
Indices: 79020--80424 Score: 2219
Period size: 177 Copynumber: 7.9 Consensus size: 177
79010 ATATTTCCTA
*
79020 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTT-AAGTGCAGAATGTTTTCAAATGAGATTTT
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAA-TGCAGGATGTTTTCAAATGAGATTTT
*
79084 AGAAACTAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAAGCCTA
65 AGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCT-AAGCCTA
79149 ATAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
129 ATAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * * * *
79198 GATTTGTGAGTCCTATGGGCCATCCATAAGAACTTCAATGCAGGATGTTTCCAAATGAGATTTTT
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAATGCAGGATGTTTTCAAATGAGATTTTA
* * * *
79263 GAAACCAAGCCTTCTGGGGTTTACTAATTATTTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
79328 AAAGGGGTTCAC-TGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
131 AAAGGGGTTC-CTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * *
79375 GATTTGTAAGTCCTACAGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAATGCAGGATGTTTTCAAATGAGATTTTA
* **
79440 GAAATCAAGCCTTTAGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
79505 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * *
79552 GATTTGTAAGTCCTATGGGCCATCCATAAGAACTTCAATGCAGGATGTTTCCAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAATGCAGGATGTTTTCAAATGAGATTTTA
* * * * *
79617 GAAACCAAGCCTTCAGGGGTTTACTAATTATTTTAAAATAGCTGTTAAAGGAAGCTAAGCCTAAC
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
*
79682 AAAGGGGTTCAC-TGACATCTAAGAAACTAAGCCTTCGGGGGTTTCTT
131 AAAGGGGTTC-CTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * *
79729 GATTTGTAAGTCCTACAGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAATGCAGGATGTTTTCAAATGAGATTTTA
*
79794 GAAACCAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
*
79859 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGAGGGTTTCTT
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * * * *
79906 GATATGTAAGTCCTACGAGCTATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAATGCAGGATGTTTTCAAATGAGATTTTA
* * *
79971 GAAATCAATCATTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
* *
80036 AAAGGGGTTCCTTGACAACTAAAAAACTAAGCCTTCGGGGGTTTTTT
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* *
80083 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTT-AAGTGCATGATGTTTTGAAATGAGATTTT
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAA-TGCAGGATGTTTTCAAATGAGATTTT
*
80147 AGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAA
65 AGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAA
* * * *
80212 TAAAGGGGTTCTTTCAC-ACTAAGAAACTAAGCCTTTGGGGGTTTATT
130 TAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * * * * *
80259 GATTTGTAAGTCCTACGGGCCATCCATAAGAACTTCAGTACAAGATGTTTTCAAATGATATTTAA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAATGCAGGATGTTTTCAAATGAGATTTTA
* *
80324 GAAACCAAGCCTCCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAC
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
80389 AAA-GGGTTCCTTGACAACTAAGAAACTAAGCCTTCG
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCG
80425 TGG
Statistics
Matches: 1125, Mismatches: 94, Indels: 18
0.91 0.08 0.01
Matches are distributed among these distances:
175 10 0.01
176 170 0.15
177 833 0.74
178 110 0.10
179 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (177 bp):
GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAATGCAGGATGTTTTCAAATGAGATTTTA
GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
Done.