Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006728.1 Hibiscus syriacus cultivar Beakdansim tig00016855_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: 102355
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1541 original size:24 final size:24
Alignment explanation
Indices: 1487--1541 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1477 CCACAACTCG
*
1487 TATAAATTACACCGAAGTGCCGCA
1 TATAAATTACACCGAAGTGCCACA
* * **
1511 TAGAAATTGCACCGAAGTGCCATT
1 TATAAATTACACCGAAGTGCCACA
1535 TATAAAT
1 TATAAAT
1542 GTCCCTAAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
TATAAATTACACCGAAGTGCCACA
Found at i:1590 original size:23 final size:23
Alignment explanation
Indices: 1538--1621 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 23
1528 TGCCATTTAT
* * *
1538 AAATGTCCCTAAGGATCACATAG
1 AAATGTCCCAAAGGACCACGTAG
* * * *
1561 TATTGTCCTAAAGGACCGCGTAG
1 AAATGTCCCAAAGGACCACGTAG
*
1584 AAATGTCCCGAAGGACCACGTAG
1 AAATGTCCCAAAGGACCACGTAG
* *
1607 AATTGTCCCAGAGGA
1 AAATGTCCCAAAGGA
1622 TCGTGTAGAA
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (23 bp):
AAATGTCCCAAAGGACCACGTAG
Found at i:1630 original size:46 final size:46
Alignment explanation
Indices: 1538--1631 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
1528 TGCCATTTAT
* * * *
1538 AAATGTCCCTAAGGATCACATAGTATTGTCCTAAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCACATAGAATTGTCCCAAAGGACCGCGTAG
* * * *
1584 AAATGTCCCGAAGGACCACGTAGAATTGTCCCAGAGGATCGTGTAG
1 AAATGTCCCGAAGGACCACATAGAATTGTCCCAAAGGACCGCGTAG
1630 AA
1 AA
1632 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (46 bp):
AAATGTCCCGAAGGACCACATAGAATTGTCCCAAAGGACCGCGTAG
Found at i:14766 original size:102 final size:95
Alignment explanation
Indices: 14616--14831 Score: 231
Period size: 97 Copynumber: 2.2 Consensus size: 95
14606 TTAATGATTT
* ** * *
14616 ATTTATTTCC-TTTAAAATAGAATCATACTTGATTCCCAAGAAAATAAATTCAATCTACCAGTTT
1 ATTTATTTCCTTTTAAAAAAGAATCATACAAGATTCCCAAAAAAATAAATCCAA--T--CA-TTT
* *
14680 ATTTTCTTTTGC-AAATCATG-AAAATAAATCCAACG
61 ATTTTCTTTTACAAAAT-A-GAAAAATAAATACAACG
* * *
14715 ATTTATTTCCTTTTATAAACAAGAATCATGCAAGATTCTCAAAAAAATAAATCCAATGATTTATT
1 ATTTATTTCCTTTTA-AAA-AAGAATCATACAAGATTCCCAAAAAAATAAATCCAATCATTTATT
14780 TTCTTTTACAAAATAGAAAAATAAATACAACG
64 TTCTTTTACAAAATAGAAAAATAAATACAACG
*
14812 ATTTATTTCCTTTTACAAAA
1 ATTTATTTCCTTTTAAAAAA
14832 TTGGAAACTA
Statistics
Matches: 101, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
95 2 0.02
96 3 0.03
97 44 0.44
98 5 0.05
99 10 0.10
100 5 0.05
101 3 0.03
102 29 0.29
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (95 bp):
ATTTATTTCCTTTTAAAAAAGAATCATACAAGATTCCCAAAAAAATAAATCCAATCATTTATTTT
CTTTTACAAAATAGAAAAATAAATACAACG
Found at i:14815 original size:39 final size:39
Alignment explanation
Indices: 14758--15023 Score: 263
Period size: 39 Copynumber: 6.8 Consensus size: 39
14748 GATTCTCAAA
* * *
14758 AAAATAAATCCAATGATTTATTTTCTTTTACAAAATAGA
1 AAAATAAATACAACGATTTATTTTCTTTTACAAAATAGG
* *
14797 AAAATAAATACAACGATTTATTTCCTTTTACAAAATTGG
1 AAAATAAATACAACGATTTATTTTCTTTTACAAAATAGG
* * * *
14836 AAACTAGAT-CTAATGATTTA-TTTCTTTTTATAAAATAGG
1 AAAATAAATAC-AACGATTTATTTTC-TTTTACAAAATAGG
** *
14875 AAAATAAATACAACGATTTA-TTTCTTTTTACAAACCAAG
1 AAAATAAATACAACGATTTATTTTC-TTTTACAAAATAGG
* ** *
14914 AAAATAAATACAACGATTTATTTCCTTTTACAAACCATG
1 AAAATAAATACAACGATTTATTTTCTTTTACAAAATAGG
* * * *
14953 AAAATAAATTA-TATGATTTATTTCCTTTTTCAAAATAGG
1 AAAATAAA-TACAACGATTTATTTTCTTTTACAAAATAGG
*
14992 AAAATAAATTCAACGATTTA-TTTCTTTGTACA
1 AAAATAAATACAACGATTTATTTTCTTT-TACA
15024 TATCAGAATC
Statistics
Matches: 189, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
38 11 0.06
39 172 0.91
40 6 0.03
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (39 bp):
AAAATAAATACAACGATTTATTTTCTTTTACAAAATAGG
Found at i:14969 original size:117 final size:117
Alignment explanation
Indices: 14758--15023 Score: 357
Period size: 117 Copynumber: 2.3 Consensus size: 117
14748 GATTCTCAAA
* *
14758 AAAATAAATCCAATGATTTATTT-TCTTTTACAAAATAGAAAAATAAATACAACGATTTATTTCC
1 AAAATAAATACAACGATTTATTTCT-TTTTACAAAATAGAAAAATAAATACAACGATTTATTTCC
* * *
14822 TTTTACAAAATTGGAAACTAGATCTAATGATTTATTT-CTTTTTATAAAATAGG
65 TTTTACAAAATTGGAAAATAAATCTAATGATTTATTTCCTTTTT-CAAAATAGG
14875 AAAATAAATACAACGATTTATTTCTTTTTACAAACCA-AG-AAAATAAATACAACGATTTATTTC
1 AAAATAAATACAACGATTTATTTCTTTTTACAAA--ATAGAAAAATAAATACAACGATTTATTTC
14938 CTTTTACAAACCA-T-GAAAATAAAT-TATATGATTTATTTCCTTTTTCAAAATAGG
64 CTTTTACAAA--ATTGGAAAATAAATCTA-ATGATTTATTTCCTTTTTCAAAATAGG
* *
14992 AAAATAAATTCAACGATTTATTTCTTTGTACA
1 AAAATAAATACAACGATTTATTTCTTTTTACA
15024 TATCAGAATC
Statistics
Matches: 135, Mismatches: 7, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
116 2 0.01
117 121 0.90
118 10 0.07
119 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (117 bp):
AAAATAAATACAACGATTTATTTCTTTTTACAAAATAGAAAAATAAATACAACGATTTATTTCCT
TTTACAAAATTGGAAAATAAATCTAATGATTTATTTCCTTTTTCAAAATAGG
Found at i:15093 original size:39 final size:38
Alignment explanation
Indices: 15050--15159 Score: 139
Period size: 39 Copynumber: 2.8 Consensus size: 38
15040 GATTCTTAGA
* * *
15050 AAAATAAATTTAACGATTTATTTCCTTCTACAAAACAGG
1 AAAATAAA-TCAATGATTTATTTCCTTTTACAAAACAGG
* * *
15089 AAAATAAATCATATGATTTATTTCGTTTTACACAATAGG
1 AAAATAAATCA-ATGATTTATTTCCTTTTACAAAACAGG
15128 AAAATAAACTCAATGATTTATTTCCTTTTACA
1 AAAATAAA-TCAATGATTTATTTCCTTTTACA
15160 TATCAAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.03
39 57 0.92
40 3 0.05
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (38 bp):
AAAATAAATCAATGATTTATTTCCTTTTACAAAACAGG
Found at i:15160 original size:136 final size:137
Alignment explanation
Indices: 14914--15258 Score: 446
Period size: 136 Copynumber: 2.5 Consensus size: 137
14904 ACAAACCAAG
** * *
14914 AAAATAAATACAACGATTTATTTCCTTTTACAAACCATGAAAATAAATTATATGATTTATTTCCT
1 AAAATAAATTTAACGATTTATTTCCTTTTACAAAACAGGAAAATAAATTATATGATTTATTTCCT
* * *
14979 TTTTCAAAATAGGAAAATAAATTCAACGATTTATTTCTTTGTACATATCAGAATCATACAAGATT
66 TTTACAAAATAGGAAAATAAACTCAACGATTTATTTCTTTGTACATATCAAAATCATACAAGATT
15044 CTTA-GA
131 CTTAGGA
* * *
15050 AAAATAAATTTAACGATTTATTTCCTTCTACAAAACAGGAAAATAAATCATATGATTTATTTCGT
1 AAAATAAATTTAACGATTTATTTCCTTTTACAAAACAGGAAAATAAATTATATGATTTATTTCCT
* * *
15115 TTTACACAATAGGAAAATAAACTCAATGATTTATTTCCTTT-TACATATCAAAATCATATAAGAT
66 TTTACAAAATAGGAAAATAAACTCAACGATTTATTT-CTTTGTACATATCAAAATCATACAAGAT
*
15179 TCTTAGGG
130 TCTTAGGA
* * * ** * * *
15187 AAAA-CAA-TTATCAATTTATTTATTTTTTCAAAACAGGAAAATAAATTATACGATTTATTTTCT
1 AAAATAAATTTAACGATTTATTTCCTTTTACAAAACAGGAAAATAAATTATATGATTTATTTCCT
15250 TTTAACAAA
66 TTT-ACAAA
15259 TCACAATCAT
Statistics
Matches: 180, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
135 49 0.27
136 122 0.68
137 9 0.05
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (137 bp):
AAAATAAATTTAACGATTTATTTCCTTTTACAAAACAGGAAAATAAATTATATGATTTATTTCCT
TTTACAAAATAGGAAAATAAACTCAACGATTTATTTCTTTGTACATATCAAAATCATACAAGATT
CTTAGGA
Found at i:15341 original size:98 final size:96
Alignment explanation
Indices: 15128--15349 Score: 243
Period size: 98 Copynumber: 2.3 Consensus size: 96
15118 ACACAATAGG
* * * *
15128 AAAATAAACTCAATGATTTATTTCCTTTTACATATCAAAATCATATAAGATTCTTAGGGAAAACA
1 AAAATAAACTCAATGATTTATTTCCTTTTACAAATCAAAATCATATAAGATTCATAGGAAAAAAA
* ** *
15193 ATTATCAATTTATTTATTTTTTCAAAACAGG
66 ATTATCAACTTATTTATTTCGTCAAAACAGA
* * * *
15224 AAAATAAA-TTATACGATTTATTTTCTTTTAACAAATCACAATCATATAAGATTCATA-GAAAAA
1 AAAATAAACTCA-ATGATTTATTTCCTTTT-ACAAATCAAAATCATATAAGATTCATAGGAAAAA
* * *
15287 TAAATTCATCGACTTATTTCCTTTCGT-AAAAGAGA
64 -AAATT-ATCAACTTATTT-ATTTCGTCAAAACAGA
15322 AAAATAAACTCAATGATTTATTTCCTTT
1 AAAATAAACTCAATGATTTATTTCCTTT
15350 CATAAAATAT
Statistics
Matches: 102, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
95 2 0.02
96 28 0.27
97 28 0.27
98 38 0.37
99 6 0.06
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (96 bp):
AAAATAAACTCAATGATTTATTTCCTTTTACAAATCAAAATCATATAAGATTCATAGGAAAAAAA
ATTATCAACTTATTTATTTCGTCAAAACAGA
Found at i:15343 original size:39 final size:38
Alignment explanation
Indices: 15280--15466 Score: 116
Period size: 39 Copynumber: 4.8 Consensus size: 38
15270 TAAGATTCAT
* *
15280 AGAAAAATAAATTC-ATCGACTTATTTCCTTTCGTAAAAG
1 AGAAAAATAAA-TCAAT-GATTTATTTCCTTTCATAAAAG
*
15319 AGAAAAATAAACTCAATGATTTATTTCCTTTCATAAAAT
1 AGAAAAATAAA-TCAATGATTTATTTCCTTTCATAAAAG
* *
15358 ATG-AAAATAAATCAAAAGATTTATTTTCTTATACA-AAAA-
1 A-GAAAAATAAATC-AATGATTTATTTCCTT-T-CATAAAAG
* * * * *
15397 AGGAAACTAAATTCAATGATCTT-TTTCATTTTC-CAAAAT
1 AGAAAAATAAA-TCAATGAT-TTATTTC-CTTTCATAAAAG
* * *
15436 AGGAAAATAAATCCGACGATTTATTTCCTTT
1 AGAAAAATAAAT-CAATGATTTATTTCCTTT
15467 TAAAAAATAG
Statistics
Matches: 121, Mismatches: 14, Indels: 27
0.75 0.09 0.17
Matches are distributed among these distances:
38 14 0.12
39 91 0.75
40 14 0.12
41 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (38 bp):
AGAAAAATAAATCAATGATTTATTTCCTTTCATAAAAG
Found at i:15381 original size:233 final size:231
Alignment explanation
Indices: 14968--15392 Score: 563
Period size: 233 Copynumber: 1.8 Consensus size: 231
14958 AAATTATATG
* * * *
14968 ATTTATTTCCTTTTTCAAAATAGGAAAATAAATTCAACGATTTATTTCTTTGTACATATCAGAAT
1 ATTTATTTACTTTTTCAAAACAGGAAAATAAATTCAACGATTTATTTCTTTGTACAAATCACAAT
* * * *
15033 CATACAAGATTCTTAGAAAAATAAATTTAACGATTTATTTCCTTCTACAAAACAGGAAAATAAAT
66 CATACAAGATTCATAGAAAAATAAATTCAACGACTTATTTCCTTCTA-AAAACAGAAAAATAAAT
* * * * *
15098 CATATGATTTATTTCGTTTTACACAATAGGAAAATAAACTCAATGATTTATTTCCTTTTACATAT
130 CATATGATTTATTTCCTTTCACAAAATAGGAAAATAAACTCAAAGATTTATTTCCTTATACATAT
15163 CAAAATCATATAAGATTCTTAGGGAAAACAATTATCA
195 CAAAATCATATAAGATTCTTAGGGAAAACAATTATCA
*
15200 ATTTATTTATTTTTTCAAAACAGGAAAATAAATT-ATACGATTTATTTTCTTT-TAACAAATCAC
1 ATTTATTTACTTTTTCAAAACAGGAAAATAAATTCA-ACGATTTA-TTTCTTTGT-ACAAATCAC
* * *
15263 AATCATATAAGATTCATAGAAAAATAAATTCATCGACTTATTTCCTTTCGT-AAAAGAGAAAAAT
63 AATCATACAAGATTCATAGAAAAATAAATTCAACGACTTATTTCC-TTC-TAAAAACAGAAAAAT
* * *
15327 AAACTCA-ATGATTTATTTCCTTTCATAAAATATGAAAATAAA-TCAAAAGATTTATTTTCTTAT
126 AAA-TCATATGATTTATTTCCTTTCACAAAATAGGAAAATAAACTC-AAAGATTTATTTCCTTAT
15390 ACA
189 ACA
15393 AAAAAGGAAA
Statistics
Matches: 166, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
231 1 0.01
232 42 0.25
233 116 0.70
234 6 0.04
235 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (231 bp):
ATTTATTTACTTTTTCAAAACAGGAAAATAAATTCAACGATTTATTTCTTTGTACAAATCACAAT
CATACAAGATTCATAGAAAAATAAATTCAACGACTTATTTCCTTCTAAAAACAGAAAAATAAATC
ATATGATTTATTTCCTTTCACAAAATAGGAAAATAAACTCAAAGATTTATTTCCTTATACATATC
AAAATCATATAAGATTCTTAGGGAAAACAATTATCA
Found at i:15474 original size:39 final size:39
Alignment explanation
Indices: 15322--15476 Score: 127
Period size: 39 Copynumber: 4.0 Consensus size: 39
15312 GTAAAAGAGA
* * * *
15322 AAAATAAA-CTCAATGATTTATTTCCTTTCATAAAATATG
1 AAAATAAATC-CAAAGATTTATTTCCTTTTAAAAAATAGG
* * *
15361 AAAATAAATCAAAAGATTTATTTTCTTATACAAAAA-AGG
1 AAAATAAATCCAAAGATTTATTTCCTTTTA-AAAAATAGG
* * * * **
15400 AAACTAAATTCAATGATCTT-TTTCATTTTCCAAAATAGG
1 AAAATAAATCCAAAGAT-TTATTTCCTTTTAAAAAATAGG
* *
15439 AAAATAAATCCGACGATTTATTTCCTTTTAAAAAATAG
1 AAAATAAATCCAAAGATTTATTTCCTTTTAAAAAATAG
15477 AATCATATAA
Statistics
Matches: 88, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
38 6 0.07
39 75 0.85
40 7 0.08
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (39 bp):
AAAATAAATCCAAAGATTTATTTCCTTTTAAAAAATAGG
Found at i:15744 original size:114 final size:116
Alignment explanation
Indices: 15515--15920 Score: 375
Period size: 117 Copynumber: 3.5 Consensus size: 116
15505 TTATTTCTTT
* * * * *
15515 ATTCAAGATTCTCGAGAAAATAAATTTC-ACAA-TTTATTTCCTTTAACAAA-ATACAATCATTT
1 ATTCAAGATTCTCAAGAAAACAAA-TTCAACAATTTTATTTCC-CTAACAAAGTTAAAATCATTT
** *
15577 AAGATTCTCAATAAAATAAATTTAACAATTTATTTCATT-TTA-AAAGA-TAGAATC
64 AAGATT-TCAAGGAAATAAATTAAACAATTTATTT--TTCTTACAAA-ATTAGAATC
** * * * * *
15631 ATTCGCGATTCTTAAGAAAACAAATTCGACAA-TTTATTTTCCTTATAAAGTT-AAATCATTTAA
1 ATTCAAGATTCTCAAGAAAACAAATTCAACAATTTTATTTCCCTAACAAAGTTAAAATCATTTAA
*
15694 GAATTCAAGGAAATAAATTAAACAATTTATTTTTCTTACAAAATTAGAATC
66 GATTTCAAGGAAATAAATTAAACAATTTATTTTTCTTACAAAATTAGAATC
* * * * *
15745 ATTCAAGATTCTCAAGGAAATAAATTTAATAATTTTATTTCCCTAACAAGGTTAAAATCATTCT-
1 ATTCAAGATTCTCAAGAAAACAAATTCAACAATTTTATTTCCCTAACAAAGTTAAAATCATT-TA
* * * *
15809 AGATTTTCAAGGAAATAAATTCAACGATTTATTTTCCTTACAAAGTTAGAATC
65 AGA-TTTCAAGGAAATAAATTAAACAATTTATTTTTCTTACAAAATTAGAATC
* * * * * *
15862 ATTTAAGATTCTCAAGGAAATAAATTTAATAA-TTTATTTCCACT-ACAAAGTTAGAATCA
1 ATTCAAGATTCTCAAGAAAACAAATTCAACAATTTTATTTCC-CTAACAAAGTTAAAATCA
15921 AACGTAAGAT
Statistics
Matches: 245, Mismatches: 35, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
112 2 0.01
113 4 0.02
114 59 0.24
115 37 0.15
116 65 0.27
117 78 0.32
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.37
Consensus pattern (116 bp):
ATTCAAGATTCTCAAGAAAACAAATTCAACAATTTTATTTCCCTAACAAAGTTAAAATCATTTAA
GATTTCAAGGAAATAAATTAAACAATTTATTTTTCTTACAAAATTAGAATC
Found at i:15909 original size:58 final size:57
Alignment explanation
Indices: 15519--15920 Score: 382
Period size: 58 Copynumber: 6.9 Consensus size: 57
15509 TTCTTTATTC
* * * * *
15519 AAGATTCTCGAGAAAATAAATTTCACAATTTATTTCCTTTAACAAA-ATACAATCATTT
1 AAGATTCTCAAGGAAATAAATTTAACAATTTATTTCC-TT-ACAAAGTTAGAATCATTT
** * * *
15577 AAGATTCTCAATAAAATAAATTTAACAATTTATTTCATTTTA-AAAGATAGAATCATTC
1 AAGATTCTCAAGGAAATAAATTTAACAATTTATTTC--CTTACAAAGTTAGAATCATTT
** * * * ** *
15635 GCGATTCTTAAGAAAACAAATTCGACAATTTATTTTCCTTATAAAGTTA-AATCATTT
1 AAGATTCTCAAGGAAATAAATTTAACAATTTA-TTTCCTTACAAAGTTAGAATCATTT
* * * * *
15692 AAGAAT-TCAAGGAAATAAATTAAACAATTTATTTTTCTTACAAAATTAGAATCATTC
1 AAGATTCTCAAGGAAATAAATTTAACAATTTA-TTTCCTTACAAAGTTAGAATCATTT
* * * *
15749 AAGATTCTCAAGGAAATAAATTTAATAATTTTATTTCCCTAACAAGGTTAAAATCATTCT
1 AAGATTCTCAAGGAAATAAATTTAACAA-TTTATTT-CCTTACAAAGTTAGAATCATT-T
* * *
15809 -AGATTTTCAAGGAAATAAATTCAACGATTTATTTTCCTTACAAAGTTAGAATCATTT
1 AAGATTCTCAAGGAAATAAATTTAACAATTTA-TTTCCTTACAAAGTTAGAATCATTT
* *
15866 AAGATTCTCAAGGAAATAAATTTAATAATTTATTTCCACTACAAAGTTAGAATCA
1 AAGATTCTCAAGGAAATAAATTTAACAATTTATTTCC-TTACAAAGTTAGAATCA
15921 AACGTAAGAT
Statistics
Matches: 282, Mismatches: 49, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
56 34 0.12
57 34 0.12
58 162 0.57
59 52 0.18
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.37
Consensus pattern (57 bp):
AAGATTCTCAAGGAAATAAATTTAACAATTTATTTCCTTACAAAGTTAGAATCATTT
Found at i:15960 original size:61 final size:57
Alignment explanation
Indices: 15662--15962 Score: 216
Period size: 58 Copynumber: 5.2 Consensus size: 57
15652 AAATTCGACA
* * ** * * **
15662 ATTTATTTTCCTTATAAAGTTA-AATCATTTAAGAAT-TCAAGGAAATAAATTAAACA
1 ATTTA-TTTCCCTACAAAGTTAGAATCACGTAAGATTCTCAAGGAAATAAATTCAATG
* * * * * *
15718 ATTTATTTTTCTTACAAAATTAGAATCA-TTCAAGATTCTCAAGGAAATAAATTTAATA
1 ATTTA-TTTCCCTACAAAGTTAGAATCACGT-AAGATTCTCAAGGAAATAAATTCAATG
* * * *
15776 ATTTTATTTCCCTAACAAGGTTAAAATCATTC-T-AGATTTTCAAGGAAATAAATTCAACG
1 A-TTTATTTCCCT-ACAAAGTTAGAATCA--CGTAAGATTCTCAAGGAAATAAATTCAATG
* ** * *
15835 ATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGGAAATAAATTTAATA
1 ATTTA-TTTCCCTACAAAGTTAGAATCACGTAAGATTCTCAAGGAAATAAATTCAATG
* * * *
15893 ATTTATTTCCACTACAAAGTTAGAATCAAACGTAAGATTCTACGATGAAATAAATCCAGTG
1 ATTTATTTCC-CTACAAAGTTAGAATC--ACGTAAGATTCT-CAAGGAAATAAATTCAATG
15954 ATTTATTTC
1 ATTTATTTC
15963 TTTATATTTT
Statistics
Matches: 198, Mismatches: 32, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
56 21 0.11
57 16 0.08
58 83 0.42
59 45 0.23
60 10 0.05
61 23 0.12
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (57 bp):
ATTTATTTCCCTACAAAGTTAGAATCACGTAAGATTCTCAAGGAAATAAATTCAATG
Found at i:16144 original size:45 final size:44
Alignment explanation
Indices: 16084--16232 Score: 185
Period size: 45 Copynumber: 3.3 Consensus size: 44
16074 TTTTACCGAC
* * *
16084 CCAATAATCACAAGGAACTAATCATTTGATTTTAATTTTCGCAAT
1 CCAATAACCAAAAGGAACTAATCATTTGATTTTACTTTT-GCAAT
*
16129 CCAATAACCGAAAGGAACTAAT-ACTTTGATTTTACTTTTTGCAA-
1 CCAATAACCAAAAGGAACTAATCA-TTTGATTTTAC-TTTTGCAAT
*
16173 CACAATAACCAAAAGGAACTAATCTTTTGATTTTACTTTTGACAAT
1 C-CAATAACCAAAAGGAACTAATCATTTGATTTTACTTTTG-CAAT
*
16219 CCAATAATCAAAAG
1 CCAATAACCAAAAG
16233 CCTAGGATTA
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
44 7 0.08
45 79 0.87
46 5 0.05
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (44 bp):
CCAATAACCAAAAGGAACTAATCATTTGATTTTACTTTTGCAAT
Found at i:16651 original size:12 final size:12
Alignment explanation
Indices: 16636--16677 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
16626 AAACACTATA
16636 TGAACAGTACCG
1 TGAACAGTACCG
* *
16648 TGAACAATA--A
1 TGAACAGTACCG
16658 TGAACAGTACCG
1 TGAACAGTACCG
16670 TGAACAGT
1 TGAACAGT
16678 GATGAACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:16695 original size:22 final size:22
Alignment explanation
Indices: 16635--16687 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
16625 GAAACACTAT
16635 ATGAACAGTACCGTGAACAATA
1 ATGAACAGTACCGTGAACAATA
* *
16657 ATGAACAGTACCGTGAACAGTG
1 ATGAACAGTACCGTGAACAATA
16679 ATGAACAGT
1 ATGAACAGT
16688 TGCGTGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (22 bp):
ATGAACAGTACCGTGAACAATA
Found at i:17756 original size:32 final size:32
Alignment explanation
Indices: 17628--17753 Score: 143
Period size: 31 Copynumber: 4.0 Consensus size: 32
17618 AACCTCGGCA
* *
17628 ACTGTCCATAGGTCCCG-AAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCGAAAG-ACATAGGTAAT
* ***
17659 ACTGTTCATATGTTCTTTAAA-ACATAGGT-AT
1 ACTGTCCATATG-TCCCGAAAGACATAGGTAAT
17690 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
*
17722 TCTGTCCATATGTCCCGAAAGACATAGGTAAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAAT
17754 TCTTCGACTC
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
30 6 0.08
31 36 0.46
32 35 0.44
33 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (32 bp):
ACTGTCCATATGTCCCGAAAGACATAGGTAAT
Found at i:18037 original size:2 final size:2
Alignment explanation
Indices: 18030--18127 Score: 178
Period size: 2 Copynumber: 49.0 Consensus size: 2
18020 TCTCATATTC
* *
18030 AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18072 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18114 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
18128 GGTTCACTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18889 original size:20 final size:20
Alignment explanation
Indices: 18864--18909 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
18854 CGAAATATCC
18864 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
18884 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
18904 ATGCAT
1 ATGCAT
18910 ATAGAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:24875 original size:19 final size:20
Alignment explanation
Indices: 24851--24897 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
24841 TTAATAATAG
*
24851 AAATATATGTTT-TTTATAT
1 AAATATATGTTTATTTATAC
*
24870 AAATATGT-TTTATTTATAC
1 AAATATATGTTTATTTATAC
24889 AAATATATG
1 AAATATATG
24898 ATGTTTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (20 bp):
AAATATATGTTTATTTATAC
Found at i:25181 original size:5 final size:5
Alignment explanation
Indices: 25165--25246 Score: 128
Period size: 5 Copynumber: 16.4 Consensus size: 5
25155 AGAATCACTC
* * *
25165 TGAAT TGTAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAA TGAAA
1 TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT
*
25215 TGAAT TGAAA TGAAT TGAAT TGAAT TGAAT TG
1 TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TG
25247 CACGGACATG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 71 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
TGAAT
Found at i:28197 original size:20 final size:19
Alignment explanation
Indices: 28172--28213 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
28162 ATTATTATGT
* *
28172 TTAATTAATATTATGTAAAA
1 TTAATTAACAATAT-TAAAA
28192 TTAATTAACAATATTAAAA
1 TTAATTAACAATATTAAAA
28211 TTA
1 TTA
28214 CAATTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAATTAACAATATTAAAA
Found at i:34900 original size:21 final size:21
Alignment explanation
Indices: 34883--34981 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
34873 CGCGTTGCAT
34883 TTCGCGTTGCGATAGTTGAAAA
1 TTCGCGTTGCGATAGTTG-AAA
34905 TT-GCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* *** * ** *
34925 ATCGCAACGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
34945 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
*
34966 ATCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
34982 CTACAGTTGT
Statistics
Matches: 58, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.28
21 40 0.69
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTTGAAA
Found at i:34999 original size:22 final size:22
Alignment explanation
Indices: 34970--35022 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
34960 TTGAAAATCG
34970 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
34992 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
35014 CGTTGCGAT
1 CGTTGCGAT
35023 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:35663 original size:6 final size:6
Alignment explanation
Indices: 35647--35690 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
35637 TCTCGTCTCG
35647 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
35691 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:35785 original size:19 final size:19
Alignment explanation
Indices: 35761--35804 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
35751 TTAACTATCG
35761 CAACGAATTTGGAAAATCA
1 CAACGAATTTGGAAAATCA
*
35780 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCA
35799 CAACGA
1 CAACGA
35805 CAACGCGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCA
Found at i:35830 original size:20 final size:20
Alignment explanation
Indices: 35805--35873 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
35795 ATCGCAACGA
35805 CAACGCGAACTGGAAAATCG
1 CAACGCGAACTGGAAAATCG
* *
35825 CAACGCGAAATGAAAAATCG
1 CAACGCGAACTGGAAAATCG
35845 CAACGCGAACTGGAAAATCG
1 CAACGCGAACTGGAAAATCG
35865 CAACGCGAA
1 CAACGCGAA
35874 ATGCAACACG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.43, C:0.25, G:0.23, T:0.09
Consensus pattern (20 bp):
CAACGCGAACTGGAAAATCG
Found at i:39276 original size:32 final size:32
Alignment explanation
Indices: 39239--39338 Score: 137
Period size: 32 Copynumber: 3.1 Consensus size: 32
39229 CCTAAGGTGA
* * *
39239 CCTTGGGTAGGCTCTAAGGCCCTAAGACATTT
1 CCTTGGGTAGGCTCTTAGGCCCTAAGACACTC
* *
39271 CCTTGGGTAGGATCTTAGGCCCTAAGATACTC
1 CCTTGGGTAGGCTCTTAGGCCCTAAGACACTC
* *
39303 CCTTGGGTAGGCTCTTAGGCCCTAAGATAATC
1 CCTTGGGTAGGCTCTTAGGCCCTAAGACACTC
39335 CCTT
1 CCTT
39339 AGGTTGGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTTAGGCCCTAAGACACTC
Found at i:43687 original size:12 final size:12
Alignment explanation
Indices: 43672--43696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43662 GAACGTGATC
43672 GAGATAGGGATA
1 GAGATAGGGATA
43684 GAGATAGGGATA
1 GAGATAGGGATA
43696 G
1 G
43697 GGATCGATAT
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:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
GAGATAGGGATA
Found at i:43695 original size:18 final size:18
Alignment explanation
Indices: 43674--43711 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43664 ACGTGATCGA
43674 GATAGGGATAGAGATAGG
1 GATAGGGATAGAGATAGG
* *
43692 GATAGGGATCGATATAGG
1 GATAGGGATAGAGATAGG
43710 GA
1 GA
43712 AGACAGAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.42, T:0.18
Consensus pattern (18 bp):
GATAGGGATAGAGATAGG
Found at i:46738 original size:3 final size:3
Alignment explanation
Indices: 46727--46787 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
46717 TTTTTTTCCG
** *
46727 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46772 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
46788 CAATTTTTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47321 original size:19 final size:19
Alignment explanation
Indices: 47294--47341 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
47284 CAAAGGAAAC
47294 GAAAGAAAAAAAGAGAGAA
1 GAAAGAAAAAAAGAGAGAA
*
47313 -AACAGAAAAAAGGAGAGAA
1 GAA-AGAAAAAAAGAGAGAA
47332 GAAAGAAAAA
1 GAAAGAAAAA
47342 TTTTACCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 22 0.85
20 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAAAGAGAGAA
Found at i:49603 original size:16 final size:16
Alignment explanation
Indices: 49569--49611 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
49559 AACGTAGACC
*
49569 AAATTTTTGTCTTATA
1 AAATTTTTTTCTTATA
49585 AAATTATTTTTCTTA-A
1 AAATT-TTTTTCTTATA
49601 AAATTGTTTTT
1 AAATT-TTTTT
49612 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
AAATTTTTTTCTTATA
Found at i:61749 original size:43 final size:42
Alignment explanation
Indices: 61700--61839 Score: 122
Period size: 46 Copynumber: 3.2 Consensus size: 42
61690 CCAGATCTCT
* *
61700 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACC-TAGATAACCAGTCGTCC
* * * ** *
61743 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-TCT
1 TCATCACGTAAGAGCCGTGTCA--ACC--TAGATAACCAG-TCGTCC
*
61789 TCATCACGTAAGAGCCGTGTCAA-CTTGATAACCAGTCGTCC
1 TCATCACGTAAGAGCCGTGTCAACCTAGATAACCAGTCGTCC
*
61830 TCATTACGTA
1 TCATCACGTA
61840 GGAACCGAGT
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
40 2 0.03
41 19 0.25
43 20 0.26
44 1 0.01
45 3 0.04
46 30 0.39
47 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (42 bp):
TCATCACGTAAGAGCCGTGTCAACCTAGATAACCAGTCGTCC
Found at i:61852 original size:87 final size:90
Alignment explanation
Indices: 61688--61899 Score: 295
Period size: 89 Copynumber: 2.4 Consensus size: 90
61678 GTCATCCCCA
*
61688 GACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
* **
61753 GGAACCGTGTTATCA-CCTTTAGAT
66 GGAACCGAGTTATCACCCTAAAGAT
* * * *
61777 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAA-C-TTGATAACCAGTCGTCCTCATTACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
61840 GGAACCGAGTTATCATCCCTAAAGAT
66 GGAACCGAGTTATCA-CCCTAAAGAT
* * *
61866 GACCAGATTTCCTCATCACGTAGGAGCCGTGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
61900 CCCTTAGACG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
87 38 0.35
88 1 0.01
89 70 0.64
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (90 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTAAAGAT
Found at i:62111 original size:3 final size:3
Alignment explanation
Indices: 62100--62160 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
62090 TTTTTTTCCG
** *
62100 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62145 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
62161 CAATTTTTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62693 original size:19 final size:19
Alignment explanation
Indices: 62666--62713 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
62656 CAAAGGAAAC
62666 GAAAGAAAAAAAGAGAGAA
1 GAAAGAAAAAAAGAGAGAA
*
62685 -AACAGAAAAAAGGAGAGAA
1 GAA-AGAAAAAAAGAGAGAA
62704 GAAAGAAAAA
1 GAAAGAAAAA
62714 TTTTACCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 22 0.85
20 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAAAGAGAGAA
Found at i:64976 original size:16 final size:16
Alignment explanation
Indices: 64942--64984 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
64932 AACGTAGACC
*
64942 AAATTTTTGTCTTATA
1 AAATTTTTTTCTTATA
64958 AAATTATTTTTCTTA-A
1 AAATT-TTTTTCTTATA
64974 AAATTGTTTTT
1 AAATT-TTTTT
64985 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
AAATTTTTTTCTTATA
Found at i:76433 original size:36 final size:36
Alignment explanation
Indices: 76392--76464 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 36
76382 ATTGATTTGT
76392 TCTGATATTTGAAATTGATAGG-TAGTCACAAAAGGA
1 TCTGATATTTG-AATTGATAGGTTAGTCACAAAAGGA
76428 TCTGATATTTGAATTGATAGGTTAGTCACAAAAGGA
1 TCTGATATTTGAATTGATAGGTTAGTCACAAAAGGA
76464 T
1 T
76465 TGGATGTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 10 0.28
36 26 0.72
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (36 bp):
TCTGATATTTGAATTGATAGGTTAGTCACAAAAGGA
Found at i:78592 original size:21 final size:21
Alignment explanation
Indices: 78563--78617 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
78553 ATTCTGACTA
78563 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
78584 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
78605 TCGCATTGCGATT
1 TCGCATTGCGATT
78618 CTCTCGTTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:80674 original size:22 final size:20
Alignment explanation
Indices: 80621--80681 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
80611 TTTTGGTGCA
*
80621 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATACCCCCTT
* * *
80641 GAGGGAACCGATTCCCCTTT
1 GAGGGAATCGATACCCCCTT
80661 GAAGGGGAATCGATACCCCCT
1 G-A-GGGAATCGATACCCCCT
80682 GGGGTTTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 18 0.55
21 1 0.03
22 14 0.42
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCTT
Found at i:84247 original size:14 final size:14
Alignment explanation
Indices: 84228--84262 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
84218 TCAATTAAAT
84228 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
84242 AAATCATCTTTTAC
1 AAATCAACATTTAC
84256 AAATCAA
1 AAATCAA
84263 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:85741 original size:42 final size:42
Alignment explanation
Indices: 85662--85754 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
85652 CCTCTTCAAC
* * *
85662 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
85704 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
85746 GATGACAGG
1 GATGACAGG
85755 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:86257 original size:20 final size:20
Alignment explanation
Indices: 86234--86342 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
86224 GAAACTTAAA
86234 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
86254 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
86274 ATTGTAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
86294 ATTGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* * **
86314 ATTGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
86334 ATCGCAACG
1 ATCGCAACG
86343 AGAGAATCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:86306 original size:40 final size:40
Alignment explanation
Indices: 86237--86342 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
86227 ACTTAAAATC
*
86237 GCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATT
1 GCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATT
* * * **
86277 GTAATGCGAAAATGACTATTGCAATGCGAATTTGACTATT
1 GCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATT
**
86317 GCAATGCGAATTTGACTATCGCAACG
1 GCAATGCGAAAATGACTATCGCAACG
86343 AGAGAATCGC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (40 bp):
GCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATT
Found at i:86410 original size:20 final size:20
Alignment explanation
Indices: 86385--86436 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
86375 GCGATTCTCT
86385 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
*
86405 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCA
*
86425 CATTGCGATAGT
1 CGTTGCGATAGT
86437 AAACTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:86596 original size:22 final size:21
Alignment explanation
Indices: 86556--86596 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
86546 CAGTATTGGC
*
86556 AGCAATCGAATGAATTTACTA
1 AGCAATCGAATGAAATTACTA
*
86577 AGCAATCTAAGTGAAATTAC
1 AGCAATCGAA-TGAAATTAC
86597 GAGTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (21 bp):
AGCAATCGAATGAAATTACTA
Found at i:88349 original size:20 final size:20
Alignment explanation
Indices: 88326--88414 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
88316 CTGAAACTTT
88326 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
88346 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
88366 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
**
88386 CTATCGCAACACG-AAATGA
1 AAATCGCAACACGAAAATGA
88405 AAATCGCAAC
1 AAATCGCAAC
88415 GACAGAATCG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 47 0.80
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:88815 original size:22 final size:22
Alignment explanation
Indices: 88753--88818 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
88743 TGACCGTGAA
* *
88753 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
88775 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
88797 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
88819 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:89038 original size:20 final size:20
Alignment explanation
Indices: 89015--89087 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
89005 CGATAGTCAG
*
89015 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
89035 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
89055 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
89075 ATTCGCATTGCGA
1 ATTCGCATTGCGA
89088 ATTAGGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:89108 original size:21 final size:21
Alignment explanation
Indices: 89084--89124 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
89074 TATTCGCATT
89084 GCGAA-TTAGGAAAATCGCAAC
1 GCGAATTTA-GAAAATCGCAAC
89105 GCGAATTTAGAAAATCGCAA
1 GCGAATTTAGAAAATCGCAA
89125 TGTGATAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:90725 original size:5 final size:5
Alignment explanation
Indices: 90717--90744 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
90707 TATTATATGT
90717 ATGCC ATGCC ATGCC ATGCC ATGCC ATG
1 ATGCC ATGCC ATGCC ATGCC ATGCC ATG
90745 ATCAAGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (5 bp):
ATGCC
Found at i:91802 original size:20 final size:21
Alignment explanation
Indices: 91779--91828 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
91769 TTACCGGGTT
91779 TTATATTTTTATTT-TTATTA
1 TTATATTTTTATTTATTATTA
*
91799 TTATA-ATTTATTTATTATTA
1 TTATATTTTTATTTATTATTA
*
91819 TTATTTTTTT
1 TTATATTTTT
91829 TTGCAGGTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 7 0.28
20 15 0.60
21 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTTATTATTA
Found at i:93493 original size:17 final size:17
Alignment explanation
Indices: 93471--93503 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
93461 CGAGATCATA
93471 ATACTAT-TTTTCATATT
1 ATACTATATTTT-ATATT
93488 ATACTATATTTTATAT
1 ATACTATATTTTATAT
93504 AAGTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (17 bp):
ATACTATATTTTATATT
Found at i:98487 original size:76 final size:74
Alignment explanation
Indices: 98375--98543 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 74
98365 AACAGTGGGG
* * ** *
98375 GGGAATCGATACCCCCTGGGGGGAATCGGTTCCCTCCGAGCACACTGTTATTTCTCGGAGCAAAA
1 GGGAATCGGTACCCCCTGGGAGGAATCGGTTCCCTCCGAGCACACTGGAATTTCTCGAAGCAAAA
98440 CAATTCAGA
66 CAATTCAGA
* *
98449 GGGAATCGGTACCCCCTTAGGGAGGAATCGGTTCCCTCCGAGCATACTGGAATTTCTCGAAGCCA
1 GGGAATCGGTACCCCC-T-GGGAGGAATCGGTTCCCTCCGAGCACACTGGAATTTCTCGAAGCAA
* *
98514 AACCATTCAGG
64 AACAATTCAGA
* *
98525 GGGAATCGGTTCCCTCTGG
1 GGGAATCGGTACCCCCTGG
98544 ACAAACTGTA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
74 17 0.21
75 2 0.02
76 63 0.77
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (74 bp):
GGGAATCGGTACCCCCTGGGAGGAATCGGTTCCCTCCGAGCACACTGGAATTTCTCGAAGCAAAA
CAATTCAGA
Found at i:101392 original size:22 final size:23
Alignment explanation
Indices: 101346--101403 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
101336 TCCCCTAAGT
*
101346 GGAATCGGTTCCGCTTCAAAGGG
1 GGAATCGGTTCCCCTTCAAAGGG
*
101369 GGAATCGGTTCCCCTT-TAAGGG
1 GGAATCGGTTCCCCTTCAAAGGG
* *
101391 GGTATCGATTCCC
1 GGAATCGGTTCCC
101404 TTTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (23 bp):
GGAATCGGTTCCCCTTCAAAGGG
Done.