Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003184.1 Hibiscus syriacus cultivar Beakdansim tig00006700_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: 82920
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:1310 original size:86 final size:84
Alignment explanation
Indices: 1220--1641 Score: 308
Period size: 86 Copynumber: 4.9 Consensus size: 84
1210 AAAAAGGATT
* *
1220 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGAGGACTCAATTT
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGAGGCCTCAATTA
1284 TAAAGGAAAAATGTGGTATTG-
66 TAAA-GAAAAA-GTGG-ATTGA
* * *
1305 AAAAAATTAGGGAG-CT-ACATTGTATAA-GTAAAAGGTG-GTATTGAAAAAATTAGGGGCCTCA
1 AAAAAATTAGGG-GCCTCA-ATTATA-AAGGTAAAAAGTGAG-ATTGAAAAAATTAGAGGCCTCA
** * *
1366 ATTATAATTATTACAAGTGAGATTAA
62 ATTATAA--AGAAAAAGTG-GATTGA
* * *
1392 AAAAAATTAAGGGCCTCAATTGTAAAGGTAAAAAGTGAGATTGCAAAAAATAAGA-G-CTCAATT
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTG-AAAAAATTAGAGGCCTCAATT
1455 ATAAAGATAAAAAGTGGGATTGA
65 ATAAAG--AAAAAGT-GGATTGA
* * * * *
1478 AAAAAATTA-AGGCAATCAATTATATATGTAAAAAAGTGAGATTAAAAAAATTA-AGAGCCTCAA
1 AAAAAATTAGGGGC-CTCAATTATAAAGGT-AAAAAGTGAGATTGAAAAAATTAGAG-GCCTCAA
** * *
1541 TTATAAAGACAAAAGATCAAATAA
63 TTATAAAGA-AAAAG-TGGATTGA
* ** * * * * *
1565 AAAAAATTTAAGGTACTCAATTATAAAGATAAAAAGTAAAATTAAAAAAAATTAGA-GCCTTCTA
1 AAAAAA-TTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATT-GAAAAAATTAGAGGCC-TCAA
1629 TTATAAAGAAAAA
63 TTATAAAGAAAAA
1642 AAAGTTAAAT
Statistics
Matches: 270, Mismatches: 38, Indels: 56
0.74 0.10 0.15
Matches are distributed among these distances:
84 3 0.01
85 35 0.13
86 84 0.31
87 84 0.31
88 62 0.23
89 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (84 bp):
AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGAGGCCTCAATTA
TAAAGAAAAAGTGGATTGA
Found at i:1406 original size:44 final size:44
Alignment explanation
Indices: 1220--1687 Score: 310
Period size: 44 Copynumber: 10.8 Consensus size: 44
1210 AAAAAGGATT
* *
1220 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATT--
1 AAAAAATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGA
* * *
1262 AAAAAATT-AGAGGACTCAATTTTAAAGGA-AAAATGTG-GTATTG-
1 AAAAAATTAAG-GGCCTCAATTATAAA-GATAAAAAGTGAG-ATTGA
* * *
1305 AAAAAATT-AGGGAGCT-ACATTGTATAAG-TAAAAGGTG-GTATTG-
1 AAAAAATTAAGGG-CCTCA-ATTATA-AAGATAAAAAGTGAG-ATTGA
* ** * * *
1348 AAAAAATTAGGGGCCTCAATTATAATTATTACAAGTGAGATTAA
1 AAAAAATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGA
* * *
1392 AAAAAATTAAGGGCCTCAATTGTAAAGGTAAAAAGTGAGATTGC
1 AAAAAATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGA
* *
1436 AAAAAA-TAAGAG-CTCAATTATAAAGATAAAAAGTGGGATTGA
1 AAAAAATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGA
* *
1478 AAAAAATTAA-GGCAATCAATTATATATG-TAAAAAAGTGAGATT-A
1 AAAAAATTAAGGGC-CTCAATTATA-AAGAT-AAAAAGTGAGATTGA
* * * * *
1522 AAAAAATTAAGAGCCTCAATTATAAAGA-CAAAAGATCA-AATAA
1 AAAAAATTAAGGGCCTCAATTATAAAGATAAAAAG-TGAGATTGA
** * * *
1565 AAAAAATTTAAGGTACTCAATTATAAAGATAAAAAGTAAAATTAA
1 AAAAAA-TTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGA
* * * * * *
1610 AAAAAATT-AGAGCCTTCTATTATAAAGAAAAAAAAGTTA-AATGG
1 AAAAAATTAAGGGCC-TCAATTATAAAG-ATAAAAAGTGAGATTGA
* * *
1654 AAAAAATTAAAGGACTCAATTATAAAAATAAAAA
1 AAAAAATTAAGGGCCTCAATTATAAAGATAAAAA
1688 ATTAGGAGTA
Statistics
Matches: 336, Mismatches: 62, Indels: 55
0.74 0.14 0.12
Matches are distributed among these distances:
41 2 0.01
42 75 0.22
43 84 0.25
44 132 0.39
45 43 0.13
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (44 bp):
AAAAAATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGA
Found at i:1497 original size:130 final size:130
Alignment explanation
Indices: 1215--1548 Score: 343
Period size: 130 Copynumber: 2.6 Consensus size: 130
1205 AAAGTAAAAA
* * * * *
1215 GGATT-AAAAAATTAGGGGCCTCAATTATAAAGGT-AAAAAGTGAGATT-AAAAAATT-AGAGGA
1 GGATTGAAAAAATTAGAGGCATCAATTATATATGTAAAAAAGTGAGATTAAAAAAATTAAG-GGC
* * * *
1276 CTCAATTTTAAAGGAAAAATGTGGTATTGAAAAAATTAGGGAGCTACATTGTATAAGTAAAAGGT
65 CTCAATTATAAAGGAAAAATGTGGTATTGAAAAAATTAGAGAGCTACATTATATAAGTAAAAAGT
1341 G
130 G
* * * * *
1342 GTATTGAAAAAATTAGGGGCCTCAATTATA-AT-TATTACAAGTGAGATTAAAAAAAATTAAGGG
1 GGATTGAAAAAATTAGAGGCATCAATTATATATGTA-AAAAAGTGAGATT-AAAAAAATTAAGGG
*
1405 CCTCAATTGTAAAGGTAAAAA-GTGAG-ATTGCAAAAAA-TA-AGAGCT-CAATTATA-AAGATA
64 CCTCAATTATAAAGG-AAAAATGTG-GTATTG-AAAAAATTAGAGAGCTAC-ATTATATAAG-TA
1464 AAAAGTG
124 AAAAGTG
*
1471 GGATTGAAAAAAATTA-AGGCAATCAATTATATATGTAAAAAAGTGAGATTAAAAAAATTAAGAG
1 GGATTG-AAAAAATTAGAGGC-ATCAATTATATATGTAAAAAAGTGAGATTAAAAAAATTAAGGG
1535 CCTCAATTATAAAG
64 CCTCAATTATAAAG
1549 ACAAAAGATC
Statistics
Matches: 176, Mismatches: 16, Indels: 27
0.80 0.07 0.12
Matches are distributed among these distances:
126 1 0.01
127 5 0.03
128 39 0.22
129 26 0.15
130 76 0.43
131 27 0.15
132 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (130 bp):
GGATTGAAAAAATTAGAGGCATCAATTATATATGTAAAAAAGTGAGATTAAAAAAATTAAGGGCC
TCAATTATAAAGGAAAAATGTGGTATTGAAAAAATTAGAGAGCTACATTATATAAGTAAAAAGTG
Found at i:1598 original size:88 final size:86
Alignment explanation
Indices: 1220--1687 Score: 278
Period size: 87 Copynumber: 5.4 Consensus size: 86
1210 AAAAAGGATT
* * * *
1220 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATT--AAAAAATT-AGAGGACTCAAT
1 AAAAAATTA-AGGACTCAATTATAAAGATAAAAAGTGAGATTAAAAAAAATTAAGA-GCCTCAAT
* * * *** **
1282 TTTAAAGGAAAAATGTGGTATTG
64 TATAAAGAAAAAAAGTCAAATAA
* * * * * *
1305 AAAAAATTAGGGAGCT-ACATTGTATAAG-TAAAAGGTG-GTATT-GAAAAAATTAGGGGCCTCA
1 AAAAAATTAAGGA-CTCA-ATTATA-AAGATAAAAAGTGAG-ATTAAAAAAAATTAAGAGCCTCA
** ** * * *
1366 ATTATAATTATTACAAGTGAGATTAA
62 ATTATAAAGAAAAAAAGTCA-AATAA
* * * **
1392 AAAAAATTAAGGGCCTCAATTGTAAAGGTAAAAAGTGAGATTGCAAAAAA-TAAGAG-CTCAATT
1 AAAAAATTAA-GGACTCAATTATAAAGATAAAAAGTGAGATTAAAAAAAATTAAGAGCCTCAATT
* ** * *
1455 ATAAAGATAAAAAGTGGGATTGA
65 ATAAAGAAAAAAAGT-CAAATAA
* *
1478 AAAAAATTAAGGCAATCAATTATATATG-TAAAAAAGTGAGATT-AAAAAAATTAAGAGCCTCAA
1 AAAAAATTAAGG-ACTCAATTATA-AAGAT-AAAAAGTGAGATTAAAAAAAATTAAGAGCCTCAA
*
1541 TTATAAAG-ACAAAAGATCAAATAA
63 TTATAAAGAAAAAAAG-TCAAATAA
* * *
1565 AAAAAATTTAAGGTACTCAATTATAAAGATAAAAAGTAAAATTAAAAAAAATT-AGAGCCTTCTA
1 AAAAAA-TTAAGG-ACTCAATTATAAAGATAAAAAGTGAGATTAAAAAAAATTAAGAGCC-TCAA
* **
1629 TTATAAAGAAAAAAAAGTTAAATGG
63 TTATAAAG-AAAAAAAGTCAAATAA
*
1654 AAAAAATTAAAGGACTCAATTATAAAAATAAAAA
1 AAAAAATT-AAGGACTCAATTATAAAGATAAAAA
1688 ATTAGGAGTA
Statistics
Matches: 304, Mismatches: 53, Indels: 49
0.75 0.13 0.12
Matches are distributed among these distances:
84 5 0.02
85 29 0.10
86 77 0.25
87 89 0.29
88 83 0.27
89 15 0.05
90 6 0.02
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (86 bp):
AAAAAATTAAGGACTCAATTATAAAGATAAAAAGTGAGATTAAAAAAAATTAAGAGCCTCAATTA
TAAAGAAAAAAAGTCAAATAA
Found at i:2180 original size:177 final size:176
Alignment explanation
Indices: 1880--2232 Score: 600
Period size: 177 Copynumber: 2.0 Consensus size: 176
1870 AACATTAGGG
*
1880 TAAATTACATGTTTACTACTTAAACTATCAGTTTTTATATGTTTAGTACTTAAACTTTTAATGTT
1 TAAATTACATGTTTACTACTTAAACTATCAGTTTTGATATGTTTAGTACTTAAACTTTTAATGTT
* * *
1945 TTGAAAACCATACATGAAGTAAAGTTTTTGTTTCATTTTAATACCTCACCATTGAAAAC-TTAAG
66 TTGAAAACCATACATGAAGTAAAGTATTTGTTTCATTTTAATACCCCACCACTGAAAACTTTAA-
** *
2009 TTTTTGTTTCATTTTAGTATTACGTTCAAAGTTTAGGTATTGAACGT
130 TTTTTGTTTCATTTTAGTACAACGTTCAAAGTTTAGGTACTGAACGT
2056 TAAATTACATGTTTACTACTTAAACTATCAGTTTTGATATGTTTTAGTACTTAAACTTTTAATGT
1 TAAATTACATGTTTACTACTTAAACTATCAGTTTTGATATG-TTTAGTACTTAAACTTTTAATGT
* *
2121 TTTGAAAACCATACATGAAGTAAAGTATTTGTTTCGTTTTAGTACCCCACCACTGAAAACTTTAA
65 TTTGAAAACCATACATGAAGTAAAGTATTTGTTTCATTTTAATACCCCACCACTGAAAACTTTAA
2186 TTTTTGTTTCATTTTAGTACAACGTTCAAAGTTTAGGTACTGAACGT
130 TTTTTGTTTCATTTTAGTACAACGTTCAAAGTTTAGGTACTGAACGT
2233 GTTAAGTTTT
Statistics
Matches: 166, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
176 40 0.24
177 122 0.73
178 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (176 bp):
TAAATTACATGTTTACTACTTAAACTATCAGTTTTGATATGTTTAGTACTTAAACTTTTAATGTT
TTGAAAACCATACATGAAGTAAAGTATTTGTTTCATTTTAATACCCCACCACTGAAAACTTTAAT
TTTTGTTTCATTTTAGTACAACGTTCAAAGTTTAGGTACTGAACGT
Found at i:9235 original size:4 final size:4
Alignment explanation
Indices: 9219--9255 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
9209 AAGCTCCAAG
*
9219 ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
9256 TTACATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:12897 original size:20 final size:20
Alignment explanation
Indices: 12803--13170 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
12793 GATTTTCCAT
* ** *
12803 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
12823 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
12843 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12863 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
12883 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
12903 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12923 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
12943 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
12963 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
12983 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
13003 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
13023 AATCGCAACGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
*
13042 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
13062 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
13082 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
13102 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
13122 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
13142 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
13162 AATCACAAC
1 AATCGCAAC
13171 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 36, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
18 1 0.00
19 18 0.06
20 281 0.93
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:13880 original size:24 final size:24
Alignment explanation
Indices: 13841--13887 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13831 AAATTTGGTC
13841 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
13865 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
13888 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:14079 original size:12 final size:12
Alignment explanation
Indices: 14062--14086 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14052 ATATAATCCT
14062 GAAGAAGAAAAA
1 GAAGAAGAAAAA
14074 GAAGAAGAAAAA
1 GAAGAAGAAAAA
14086 G
1 G
14087 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:16407 original size:19 final size:19
Alignment explanation
Indices: 16385--16710 Score: 380
Period size: 19 Copynumber: 18.4 Consensus size: 19
16375 CGGAAAATAC
*
16385 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
16404 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
16418 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
16438 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
16452 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16471 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16490 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
16509 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
16523 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16542 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
16561 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
16575 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
16594 AATCGCAATACGAAATG-A
1 AATCGCAATGCGAAATGAA
16612 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16631 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16650 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
16664 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
16684 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
16703 AATCGCAA
1 AATCGCAA
16711 CGAGATAATC
Statistics
Matches: 266, Mismatches: 13, Indels: 56
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.17
15 4 0.02
16 12 0.05
17 18 0.07
18 23 0.09
19 140 0.53
20 24 0.09
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:16522 original size:71 final size:71
Alignment explanation
Indices: 16385--16710 Score: 440
Period size: 71 Copynumber: 4.6 Consensus size: 71
16375 CGGAAAATAC
* *
16385 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
16445 ACGAGAG
65 ACGAGAG
16452 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
16517 CGAGAG
66 CGAGAG
* *
16523 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
* *
16583 TGCGAAATTAA
66 --CG--A-GAG
*
16594 AATCGCAATACGAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
16658 CGAAAG
66 CGAGAG
16664 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
16711 CGAGATAATC
Statistics
Matches: 230, Mismatches: 12, Indels: 29
0.85 0.04 0.11
Matches are distributed among these distances:
66 8 0.03
67 25 0.11
68 2 0.01
69 6 0.03
70 39 0.17
71 91 0.40
72 49 0.21
73 2 0.01
75 8 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAGAG
Found at i:16527 original size:52 final size:53
Alignment explanation
Indices: 16385--16710 Score: 347
Period size: 52 Copynumber: 6.2 Consensus size: 53
16375 CGGAAAATAC
* *
16385 AATCGCAACGCGAAATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATG-AAATCGCAAGCGATGAAAATCGCAATGC-GAAATGAA
*
16438 AATCGCAA--CGAGA-G-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAATCGCAA-GCG--ATGAAAATCGCAATGCGAAATGAA
*
16490 AATCGCAATGCGAAATGAAAATCGCAA-CGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-AAATCGCAAGCGATGAAAATCGCAATGCGAAATGAA
* * * *
16542 AATCGCAATGCGAAATGAAAATCG-AACCGA-CATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATG-AAATCGCAAGCGATGAAAATCGCAATGCGAAATGAA
*
16594 AATCGCAATACGAAATGAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAATCGCAA-GCG--ATGAAAATCGCAATGCGAAATGAA
16650 AATCGCAA--CGAAA-G-AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAATCGCAA-GC-G--ATGAAAATCGCAATGCGAAATGAA
16703 AATCGCAA
1 AATCGCAA
16711 CGAGATAATC
Statistics
Matches: 244, Mismatches: 12, Indels: 34
0.84 0.04 0.12
Matches are distributed among these distances:
48 7 0.03
50 2 0.01
51 12 0.05
52 112 0.46
53 63 0.26
54 9 0.04
55 4 0.02
56 27 0.11
57 8 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAATCGCAAGCGATGAAAATCGCAATGCGAAATGAA
Found at i:16725 original size:33 final size:34
Alignment explanation
Indices: 16471--16732 Score: 170
Period size: 33 Copynumber: 7.5 Consensus size: 34
16461 GCGAAATGAA
*
16471 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAT
* *
16509 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAT
* *
16542 AATCGCAATGCGAAATGAAAATCG-AACCGACAT
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAGAT
* * *
16575 AATCGCAATGCGAAATTAAAATCGCAATACGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAGAT
*
16610 GAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 --AATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAT
*
16650 AATCGCAA--CGAAA-G--AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GC-G--A-GAT
16684 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAGAT
16717 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
16733 TATAAACGCA
Statistics
Matches: 193, Mismatches: 13, Indels: 41
0.78 0.05 0.17
Matches are distributed among these distances:
33 82 0.42
34 21 0.11
35 8 0.04
36 15 0.08
37 34 0.18
38 23 0.12
39 9 0.05
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAGAT
Found at i:16829 original size:19 final size:19
Alignment explanation
Indices: 16739--16821 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
16729 AAATTATAAA
16739 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
16758 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
16778 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
16794 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
16811 CGCATTGCGAT
1 CGCATTGCGAT
16822 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:16947 original size:14 final size:14
Alignment explanation
Indices: 16928--16963 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
16918 CATCAATTAC
16928 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
16942 ACAAATCATCTTTT
1 ACAAATCAACTTTT
16956 AC-AATCAA
1 ACAAATCAA
16964 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:16973 original size:12 final size:12
Alignment explanation
Indices: 16956--17030 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
16946 ATCATCTTTT
16956 ACAATCAATTAA
1 ACAATCAATTAA
16968 ACAATCAA--AA
1 ACAATCAATTAA
* **
16978 ATTGAATCAACTTTT
1 A--CAATCAA-TTAA
16993 ACAAATCAATTAA
1 AC-AATCAATTAA
*
17006 ACAATCAA-AAA
1 ACAATCAATTAA
17017 ACAATCAATTAA
1 ACAATCAATTAA
17029 AC
1 AC
17031 TATTGAATCA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
10 3 0.06
11 10 0.21
12 24 0.50
13 4 0.08
14 6 0.12
15 1 0.02
ACGTcount: A:0.57, C:0.17, G:0.01, T:0.24
Consensus pattern (12 bp):
ACAATCAATTAA
Found at i:16992 original size:37 final size:38
Alignment explanation
Indices: 16945--17016 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
16935 AACTTTTACA
*
16945 AATCATCTTTTAC-AATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
16982 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
17017 ACAATCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 12 0.36
38 21 0.64
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:18903 original size:14 final size:14
Alignment explanation
Indices: 18884--18940 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
18874 GCGAAATGAA
*
18884 AATCGCAACGACAG
1 AATCGCAACGAAAG
18898 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
18915 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
18931 AATCGCAACG
1 AATCGCAACG
18941 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:18911 original size:33 final size:33
Alignment explanation
Indices: 18865--18957 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
18855 GCGAAACCAA
*
18865 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
18898 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
18931 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
18958 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:18922 original size:19 final size:19
Alignment explanation
Indices: 18828--18962 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
18818 TAGTTTACTT
* *
18828 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
18848 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
18867 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
18886 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
18900 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
18919 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
18933 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
18952 TCGCAATGCGA
1 TCGCAACGCGA
18963 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:18980 original size:19 final size:19
Alignment explanation
Indices: 18958--19086 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
18948 AAAATCGCAA
18958 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
18977 TGCGAACTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
18991 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
19010 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
19024 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
19043 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
19062 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
19082 TGCGA
1 TGCGA
19087 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:19048 original size:33 final size:34
Alignment explanation
Indices: 18958--19049 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 34
18948 AAAATCGCAA
*
18958 TGCGATTTTGGTTTCGCGTTGCGA-ACTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
18991 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
19024 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
19050 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.45
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:19289 original size:93 final size:93
Alignment explanation
Indices: 19130--19509 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
19120 TTGAATGGAT
19130 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
19195 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
19223 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
19288 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
19316 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
19380 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
19408 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
19473 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
19501 AAATTTACT
1 AAATTTACT
19510 AAGCAATCTA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:19443 original size:185 final size:186
Alignment explanation
Indices: 19130--19509 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
19120 TTGAATGGAT
19130 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
19195 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
19260 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
19316 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
19380 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
19445 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
19501 AAATTTACT
1 AAATTTACT
19510 AAGCAATCTA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:21232 original size:14 final size:14
Alignment explanation
Indices: 21213--21302 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
21203 TTGAAATGAA
21213 AATCGCAACGAGAG
1 AATCGCAACGAGAG
21227 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
21244 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
21260 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
21279 AATCGCAACGAGAG
1 AATCGCAACGAGAG
21293 AATCGCAACG
1 AATCGCAACG
21303 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:21250 original size:33 final size:33
Alignment explanation
Indices: 21205--21319 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
21195 TCTTTTGGTT
21205 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
21238 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
21271 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
21304 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
21320 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:21251 original size:19 final size:18
Alignment explanation
Indices: 21212--21324 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
21202 GTTGAAATGA
21212 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
21227 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
21244 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
21260 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
21277 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
21293 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
21310 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
21325 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:21553 original size:33 final size:33
Alignment explanation
Indices: 21511--21581 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
21501 AATACTAACT
*
21511 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
21544 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
21577 TGAAA
1 TGAAA
21582 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:21815 original size:22 final size:22
Alignment explanation
Indices: 21763--21817 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
21753 TGGTTGTGAG
**
21763 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
21785 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
21807 GGATTTCTTCG
1 GGATTTCTTCG
21818 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:21988 original size:20 final size:20
Alignment explanation
Indices: 21963--22155 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
21953 CTTTAAATAT
21963 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
21983 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
22005 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22024 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
22044 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
22064 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22084 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
22104 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
22124 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
22144 CGCGTTGCGATT
1 CGCGTTGCGATT
22156 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:22150 original size:60 final size:60
Alignment explanation
Indices: 21963--22155 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
21953 CTTTAAATAT
**
21963 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
22024 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
22084 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
22144 CGCGTTGCGATT
1 CGCGTTGCGATT
22156 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:22236 original size:20 final size:20
Alignment explanation
Indices: 22211--22262 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
22201 AAGAATCGCG
*
22211 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
22231 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
22251 TTGCGATTCTGG
1 TTGCGATTCTGG
22263 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:26925 original size:14 final size:14
Alignment explanation
Indices: 26908--26935 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
26898 ATCATAACAA
26908 AATTATATAACTAT
1 AATTATATAACTAT
26922 AATTATATAACTAT
1 AATTATATAACTAT
26936 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:27267 original size:17 final size:18
Alignment explanation
Indices: 27245--27278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27235 TCAGCCGGTC
27245 CGATTC-GAACGGTTCAA
1 CGATTCTGAACGGTTCAA
*
27262 CGATTCTGACCGGTTCA
1 CGATTCTGAACGGTTCA
27279 CTAATAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (18 bp):
CGATTCTGAACGGTTCAA
Found at i:28062 original size:112 final size:112
Alignment explanation
Indices: 27821--28385 Score: 919
Period size: 112 Copynumber: 5.1 Consensus size: 112
27811 TCAGTTTGTT
* * * * *
27821 TCGATACTTTATAAAAATATATTGATCTAAAACAATATAACAGGTAAAAAAATGACAAAACCAGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
27886 CTATAAATGACAAAAC------AGCGCTACCGGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
* *
27927 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACTGGTAAAAAAATGACAAAATCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
27992 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
28039 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
* * * *
28104 TTATAAATGACAAAATATGTAAAGCGCTACTGGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
* *
28151 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGT-AAAAAATGACAAAACCGAT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
28215 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
*
28262 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGC
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
* * * *
28327 CTATAAATGACAAAACAGGTAAAACGCTACCGAATATGTTGATAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
28374 TCGATACTTTAT
1 TCGATACTTTAT
28386 TATAAGTATC
Statistics
Matches: 426, Mismatches: 26, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
106 74 0.17
111 105 0.25
112 247 0.58
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (112 bp):
TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
Found at i:28272 original size:223 final size:222
Alignment explanation
Indices: 27821--28385 Score: 906
Period size: 223 Copynumber: 2.5 Consensus size: 222
27811 TCAGTTTGTT
* * * * *
27821 TCGATACTTTATAAAAATATATTGATCTAAAACAATATAACAGGTAAAAAAATGACAAAACCAGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
*
27886 CTATAAATGAC--AAA--ACAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGT
66 CTATAAATGACAAAAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGT
** * *
27947 ATCGATCCATAACAATATAACTGGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAACAGGT
131 ATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAGGT
28012 AAAGCGCTACCGGATATATTGAAAGTG
196 AAAGCGCTACCGGATATATTGAAAGTG
28039 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
* *
28104 TTATAAATGACAAAATATGTAAAGCGCTACTGGATATATTGAAAGTGTCGATACTTTATAAAAAT
66 CTATAAATGACAAAA-A-GTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAAT
28169 GTATCGATCCATAACAATATAACAAGT-AAAAAATGACAAAACCGATCTATAAATGACAAAACAG
129 GTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAG
28233 GTAAAGCGCTACCGGATATATTGAAAGTG
194 GTAAAGCGCTACCGGATATATTGAAAGTG
*
28262 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGC
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
* * * *
28327 CTATAAATGACAAAACAGGTAAAACGCTACCGAATATGTTGATAGTGTCGATACTTTAT
66 CTATAAATGACAAAA-A-GTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
28386 TATAAGTATC
Statistics
Matches: 320, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
218 70 0.22
220 2 0.01
221 1 0.00
223 179 0.56
224 68 0.21
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (222 bp):
TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
CTATAAATGACAAAAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGT
ATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAGGT
AAAGCGCTACCGGATATATTGAAAGTG
Found at i:28658 original size:162 final size:160
Alignment explanation
Indices: 28333--28663 Score: 540
Period size: 162 Copynumber: 2.1 Consensus size: 160
28323 CGGCCTATAA
* *
28333 ATGACAAAACAGGTAAAACGCTACCGAATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACAGATAAAACGCTACCGAATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
*
28398 CACTTTTGAAATTTAAAAGAAGAAGTTATATCGCTAATAAAGTGTCGATACTTTATAAAAATGTA
66 CACTTTTGAAATTTAAAAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATGTA
28463 TCGATCCATAACAATATAACAAGTAAAAAT
131 TCGATCCATAACAATATAACAAGTAAAAAT
* *
28493 ATGACAAAACCGATAAAGA-GCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
1 ATGACAAAACAGATAAA-ACGCTACCGAATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
*
28557 ACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCG-TCAATAAAGTGTCGATACTTTATAAAAA
65 ACACTTTTGAAATTTAAAAG--AAGAAGTTATAGCGCT-AATAAAGTGTCGATACTTTATAAAAA
*
28621 TGTATCGATCCATAACAATATAACATGTAAAAAT
127 TGTATCGATCCATAACAATATAACAAGTAAAAAT
*
28655 ATGATAAAA
1 ATGACAAAA
28664 TCGGTCTCAA
Statistics
Matches: 159, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
160 77 0.48
161 2 0.01
162 80 0.50
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (160 bp):
ATGACAAAACAGATAAAACGCTACCGAATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
CACTTTTGAAATTTAAAAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATGTA
TCGATCCATAACAATATAACAAGTAAAAAT
Found at i:29156 original size:23 final size:23
Alignment explanation
Indices: 29123--29170 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
29113 AAATATGTCA
*
29123 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTAATACATT
* *
29146 ATATAAGCGCTACCTAATATATT
1 ATATAAACGCTACCTAATACATT
29169 AT
1 AT
29171 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTAATACATT
Found at i:29374 original size:24 final size:23
Alignment explanation
Indices: 29330--29374 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
29320 AACTATATAT
*
29330 ATACATAACATGGATGGATGCGC
1 ATACATAACATGGATGCATGCGC
*
29353 ATACATACACATGTATGCATGC
1 ATACATA-ACATGGATGCATGC
29375 ATGTTGCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (23 bp):
ATACATAACATGGATGCATGCGC
Found at i:32440 original size:2 final size:2
Alignment explanation
Indices: 32433--32494 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
32423 GTTGAAAATA
32433 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
32475 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
32495 GAGTCTCATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33229 original size:10 final size:10
Alignment explanation
Indices: 33214--33243 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
33204 TATGAATAGC
*
33214 TTTATTTTAT
1 TTTATTTTAA
33224 TTTATTTTAA
1 TTTATTTTAA
33234 TTTATTTTAA
1 TTTATTTTAA
33244 AAGTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTTTAA
Found at i:33277 original size:16 final size:16
Alignment explanation
Indices: 33256--33286 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33246 GTAAATATAT
33256 TAAATTCAAATAAATC
1 TAAATTCAAATAAATC
*
33272 TAAATTTAAATAAAT
1 TAAATTCAAATAAAT
33287 TTAATCTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATTCAAATAAATC
Found at i:34399 original size:20 final size:20
Alignment explanation
Indices: 34374--34412 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34364 TTTTTGTTTG
*
34374 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
34394 GCCGCCGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
34413 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:36059 original size:10 final size:10
Alignment explanation
Indices: 36044--36077 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
36034 TTCATTTACC
36044 ATTTATTTTT
1 ATTTATTTTT
36054 ATTTATTTTT
1 ATTTATTTTT
* *
36064 ATCTATTTCT
1 ATTTATTTTT
36074 ATTT
1 ATTT
36078 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:45570 original size:12 final size:12
Alignment explanation
Indices: 45553--45577 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45543 ATTGAAAAAG
45553 AAAAAAGAGAAA
1 AAAAAAGAGAAA
45565 AAAAAAGAGAAA
1 AAAAAAGAGAAA
45577 A
1 A
45578 TAAGGTGGGT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:46635 original size:599 final size:599
Alignment explanation
Indices: 45497--46707 Score: 2208
Period size: 599 Copynumber: 2.0 Consensus size: 599
45487 CTAAGTTAAA
**
45497 AAAAAAAAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGAG
1 AAAAAAAAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCACCCTAAATAAAAAAAGAAAAAAGAG
45562 AAAAAAAAAGAGAAAATAAGGTGGGTTCAAGATGAAAACCCGCAAAGGGCGTCTCGCAACCAAGG
66 AAAAAAAAAGAGAAAATAAGGTGGGTTCAAGATGAAAACCCGCAAAGGGCGTCTCGCAACCAAGG
* *
45627 ATGGGTCCAAGTTGAAAACCCGGAAAGGGCGATTTGGATATTAACGGTGGAAACATCCCGGCACA
131 ATGGGTCCAAGTTGAAAACCCGGAAAGGGCAATTTGGATATCAACGGTGGAAACATCCCGGCACA
* *
45692 TGAATCTTCCACGAACTCAACAAATCGGAGAAATGTTGCACCCTCCCAAACGTTGTCGCATTTTC
196 TGAATCTTCCACGAACCCAACAAATCGGAGAAATGTCGCACCCTCCCAAACGTTGTCGCATTTTC
*
45757 AAAGATCCTTTGGCAAAGGCTGCATTCAAAGTCACCAAACGGCTTTTCAACTCAGAAGTGCCCAC
261 AAAGATCCTTTGGCAAAGGCTGCACTCAAAGTCACCAAACGGCTTTTCAACTCAGAAGTGCCCAC
*
45822 ATTATCGAGGTCTAAGACATTCATTTACACATCATTGTGTATTCGTTTTCTAGAATGTTTGCCAT
326 ATTATCGAGATCTAAGACATTCATTTACACATCATTGTGTATTCGTTTTCTAGAATGTTTGCCAT
45887 GTATTATTTGTTCTTCTCCTCCCTTATGAATAAAGACCATCTTTCCTCCAATACCTTTTGAGCAT
391 GTATTATTTGTTCTTCTCCTCCCTTATGAATAAAGACCATCTTTCCTCCAATACCTTTTGAGCAT
*
45952 CTTGAATTAGATTTAAACCTAATGGTTTATTTATTTTTATGAAAGATAATCACATATTGTTGTAC
456 CTTGAATTAGATTTAAACCTAATGGTTTATTTATTTTTATGAAAGATAATCACATATTGCTGTAC
*
46017 AAAGATTCATTGAAAAGTACAGGTACTCAGAAGCCGATCAAGGCTCATGCACATGCTTGAGATGG
521 AAAGATTCATTGAAAAGTACAGGTACCCAGAAGCCGATCAAGGCTCATGCACATGCTTGAGATGG
*
46082 TTGAGGGGCATCTT
586 TTGAGGAGCATCTT
* *
46096 TAAAAAAAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAG-AAAAAGA
1 AAAAAAAAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCACCCTAAAT-AAAAAAAGAAAAAAGA
* * * *
46160 GGAAAAAGAAGAGAAAATAAGGTGGGTTCAAGATGAAAACCCGCAAAGGGCGTCTTGCAACTAAG
65 GAAAAAAAAAGAGAAAATAAGGTGGGTTCAAGATGAAAACCCGCAAAGGGCGTCTCGCAACCAAG
46225 GATGGGTCCAAGTTGAAAACCCGGAAAGGGCAATTTGGATATCAACGGTGGAAACATCCCGGCAC
130 GATGGGTCCAAGTTGAAAACCCGGAAAGGGCAATTTGGATATCAACGGTGGAAACATCCCGGCAC
*
46290 ATGAATCTTCTACGAACCCAACAAATCGGAGAAATGTCGCACCCTCCCAAACGTTGTCGCATTTT
195 ATGAATCTTCCACGAACCCAACAAATCGGAGAAATGTCGCACCCTCCCAAACGTTGTCGCATTTT
*
46355 CAAAGATCCTTTGGCAAAGGCTGCACTCAGAGTCACCAAACGGCTTTTCAACTCAGAAGTGCCCA
260 CAAAGATCCTTTGGCAAAGGCTGCACTCAAAGTCACCAAACGGCTTTTCAACTCAGAAGTGCCCA
*
46420 CGTTATCGAGATCTAAGACATTCATTTACACATCATTGTGTATTCGTTTTCTAGAATGTTTGCCA
325 CATTATCGAGATCTAAGACATTCATTTACACATCATTGTGTATTCGTTTTCTAGAATGTTTGCCA
*
46485 TGTATTATTTGTTCTTCTCCTCCCTTATGAATAAATACCATCTTTCCTCCAATACCTTTTGAGCA
390 TGTATTATTTGTTCTTCTCCTCCCTTATGAATAAAGACCATCTTTCCTCCAATACCTTTTGAGCA
*
46550 TCTTGAATTAGATTTAAACCTAATGGTTTATTTATTTTTATGAAAGATAATCGCATATTGCTGTA
455 TCTTGAATTAGATTTAAACCTAATGGTTTATTTATTTTTATGAAAGATAATCACATATTGCTGTA
46615 CAAAGATTCATTGAAAAGTACAGGTACCCAGAAGCCGATCAAGGCTCATGCACATGCTTGAGATG
520 CAAAGATTCATTGAAAAGTACAGGTACCCAGAAGCCGATCAAGGCTCATGCACATGCTTGAGATG
46680 GTTGAGGAGCATCTT
585 GTTGAGGAGCATCTT
46695 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
46708 TCATCAAACG
Statistics
Matches: 588, Mismatches: 23, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
599 582 0.99
600 6 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (599 bp):
AAAAAAAAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCACCCTAAATAAAAAAAGAAAAAAGAG
AAAAAAAAAGAGAAAATAAGGTGGGTTCAAGATGAAAACCCGCAAAGGGCGTCTCGCAACCAAGG
ATGGGTCCAAGTTGAAAACCCGGAAAGGGCAATTTGGATATCAACGGTGGAAACATCCCGGCACA
TGAATCTTCCACGAACCCAACAAATCGGAGAAATGTCGCACCCTCCCAAACGTTGTCGCATTTTC
AAAGATCCTTTGGCAAAGGCTGCACTCAAAGTCACCAAACGGCTTTTCAACTCAGAAGTGCCCAC
ATTATCGAGATCTAAGACATTCATTTACACATCATTGTGTATTCGTTTTCTAGAATGTTTGCCAT
GTATTATTTGTTCTTCTCCTCCCTTATGAATAAAGACCATCTTTCCTCCAATACCTTTTGAGCAT
CTTGAATTAGATTTAAACCTAATGGTTTATTTATTTTTATGAAAGATAATCACATATTGCTGTAC
AAAGATTCATTGAAAAGTACAGGTACCCAGAAGCCGATCAAGGCTCATGCACATGCTTGAGATGG
TTGAGGAGCATCTT
Found at i:47276 original size:106 final size:106
Alignment explanation
Indices: 46899--47462 Score: 981
Period size: 106 Copynumber: 5.3 Consensus size: 106
46889 AGGTTTTACC
*
46899 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
46964 ACGAAGGGACCGCTGGTTGTCAACAAA-TATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
47004 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
47069 ACGAAGGGACCGCTGCTTGTCAACAAAC-ATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
*
47109 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
47174 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
*
47215 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
47280 AAGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
* *
47321 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
47386 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTC-CAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTC-AATTT
*
47427 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
47463 CCTCGGAACA
Statistics
Matches: 440, Mismatches: 16, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
105 193 0.44
106 247 0.56
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
Found at i:48852 original size:20 final size:20
Alignment explanation
Indices: 48827--48865 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48817 TTTTTGTTTG
*
48827 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
48847 GCCGCCGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
48866 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:59638 original size:13 final size:13
Alignment explanation
Indices: 59620--59646 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59610 ATTGAACGTT
59620 ATAAAAGTAATAA
1 ATAAAAGTAATAA
59633 ATAAAAGTAATAA
1 ATAAAAGTAATAA
59646 A
1 A
59647 AATGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAAAAGTAATAA
Found at i:59847 original size:18 final size:17
Alignment explanation
Indices: 59821--59862 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
59811 AAGAAAATAT
*
59821 AATAAATAAGTAAAAAC
1 AATAAATAAGTAAAAAA
59838 AATAACATAAGTAAAAAA
1 AATAA-ATAAGTAAAAAA
59856 AATAAAT
1 AATAAAT
59863 TATACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (17 bp):
AATAAATAAGTAAAAAA
Found at i:61327 original size:3 final size:3
Alignment explanation
Indices: 61319--61390 Score: 119
Period size: 3 Copynumber: 23.7 Consensus size: 3
61309 GTATATTGTA
61319 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
61365 AAT AAT AAT AAAT AAT AAT AA- AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AA
61391 ATATAAAAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.03
3 58 0.88
4 6 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:61396 original size:6 final size:5
Alignment explanation
Indices: 61318--61398 Score: 58
Period size: 6 Copynumber: 14.6 Consensus size: 5
61308 TGTATATTGT
61318 AAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAAT- AAATA ATAATA
1 AAATA A-AATA A-AATA A-AATA A-AATA A-AATA A-AATA AAATA A-AATA
61369 ATAAT- AAATA ATAATA AAATA AATATA AAA
1 A-AATA AAATA A-AATA AAATA AA-ATA AAA
61399 GACCCGGACA
Statistics
Matches: 70, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
4 6 0.09
5 12 0.17
6 52 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (5 bp):
AAATA
Found at i:61833 original size:43 final size:45
Alignment explanation
Indices: 61785--61984 Score: 131
Period size: 43 Copynumber: 4.4 Consensus size: 45
61775 ATAACTCGGT
61785 TCCTACGTGATGAGGACGGCTGATTATCTAA-GGT-TGACACGGC
1 TCCTACGTGATGAGGACGGCTGATTATCTAAGGGTATGACACGGC
* * * ** * *
61828 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGT
1 TCCTACGTGATGAGGACGGCTGATTATCTAAGGGT--ATGACACGGC
* * * * * ** * * *
61875 TCATACATGATGAAGAACTCTGGC-CATCTTTAGGAAGGGTGATAACTCGGT
1 TCCTACGTGATG-AGGA--C-GGCTGAT-TAT-CTAAGGGT-ATGACACGGC
61926 TCCTACGTGATGAGGACGGCTGATTATCTAA-GGT-TGACACGGC
1 TCCTACGTGATGAGGACGGCTGATTATCTAAGGGTATGACACGGC
61969 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
61985 AGTCTGGTCA
Statistics
Matches: 115, Mismatches: 31, Indels: 22
0.68 0.18 0.13
Matches are distributed among these distances:
43 48 0.42
44 3 0.03
45 3 0.03
46 2 0.02
47 22 0.19
48 6 0.05
50 4 0.03
51 21 0.18
52 6 0.05
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (45 bp):
TCCTACGTGATGAGGACGGCTGATTATCTAAGGGTATGACACGGC
Found at i:61942 original size:141 final size:140
Alignment explanation
Indices: 61544--61993 Score: 637
Period size: 134 Copynumber: 3.2 Consensus size: 140
61534 TGTTGGGGAC
* * * * *
61544 GACACTGCTCATACATGATGAAGAGGTCTGGTCGTCTAAGGGTGGATGACACGACTCATACGTGA
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGT-GATGACACGACTCATACGTGA
* * * *
61609 TGAAGAGTTTCTGGCCATCTTTTGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGG
65 TGAAGA-ATTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGA
*
61674 TTATCTATGGTT
129 TTATCTAAGGTT
61686 GACACGGCTCCTACGTGATGAGG-AGATCT-G--GTC---GGG-GATGACACGACTCATACGTGA
1 GACACGGCTCCTACGTGATGAGGAAG-TCTGGTCGTCTAAGGGTGATGACACGACTCATACGTGA
* * *
61743 TGAAGAGTTCTTGGACATCTTTAGGAAAGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGA
65 TGAAGAATTC-TGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGA
61808 TTATCTAAGGTT
129 TTATCTAAGGTT
* ** *
61820 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGA
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGT-GATGACACGACTCATACGTGA
*
61885 TGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGAT
65 TGAAGAATTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGAT
61950 TATCTAAGGTT
130 TATCTAAGGTT
61961 GACACGGCTCCTACGTGATGAGGAAGTCTGGTC
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTC
61994 AGTTGATGTT
Statistics
Matches: 277, Mismatches: 20, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
133 3 0.01
134 113 0.41
135 3 0.01
136 3 0.01
137 3 0.01
139 3 0.01
140 3 0.01
141 99 0.36
142 47 0.17
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (140 bp):
GACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTGATGACACGACTCATACGTGAT
GAAGAATTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATT
ATCTAAGGTT
Found at i:62029 original size:141 final size:137
Alignment explanation
Indices: 61618--62029 Score: 498
Period size: 141 Copynumber: 3.0 Consensus size: 137
61608 ATGAAGAGTT
* * * *
61618 TCTGGCCATCTTTTGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATCTATG
1 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCTAAG
** * * *
61683 GTTGACACGGCTCCTACGTGATGAGG-AGATCTGGTCGGGGATG-ACAC-GACTCA--TAC-GTG
66 GTTGACACGGCTCCTACGTGATGAGGAAG-TCTGGTCGTTGATGTAGACTGA-TCATGTTCAATG
**
61742 ATGAAGAGT
129 ATGAAGAAC
* *
61751 TCTTGGACATCTTTAGGAAAGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCTAA
1 TC-TGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCTAA
* *
61816 GGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGA-TGA-CATGGTTCAT
65 GGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCGT-TGA-TGTAGACTGATCAT-GTTC--
61879 ACATGATGAAGAAC
125 A-ATGATGAAGAAC
61893 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCTAAG
1 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCTAAG
*
61958 GTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCAGTTGATGTTGACTGATTCATTGCTTCAA
66 GTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTC-GTTGATGTAGACTGA-TCA-TG-TTCAA
*
62023 TAATGAA
127 TGATGAA
62030 ATAAATCTTG
Statistics
Matches: 239, Mismatches: 21, Indels: 30
0.82 0.07 0.10
Matches are distributed among these distances:
133 2 0.01
134 91 0.38
135 5 0.02
136 1 0.00
137 4 0.02
138 2 0.01
140 4 0.02
141 109 0.46
142 14 0.06
143 3 0.01
144 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (137 bp):
TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCTAAG
GTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTTGATGTAGACTGATCATGTTCAATGAT
GAAGAAC
Found at i:62955 original size:14 final size:14
Alignment explanation
Indices: 62938--62984 Score: 76
Period size: 14 Copynumber: 3.2 Consensus size: 14
62928 TTCTTTCTTT
62938 TTTTTTTTGATTGA
1 TTTTTTTTGATTGA
62952 TTTTTTTTGATTGA
1 TTTTTTTTGATTGA
62966 TTTTTTTTTTGATTGA
1 --TTTTTTTTGATTGA
62982 TTT
1 TTT
62985 AAGTGTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 17 0.55
16 14 0.45
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (14 bp):
TTTTTTTTGATTGA
Found at i:62955 original size:16 final size:16
Alignment explanation
Indices: 62936--62984 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
62926 TTTTCTTTCT
62936 TTTTTTTTTTGATTGA
1 TTTTTTTTTTGATTGA
62952 --TTTTTTTTGATTGA
1 TTTTTTTTTTGATTGA
62966 TTTTTTTTTTGATTGA
1 TTTTTTTTTTGATTGA
62982 TTT
1 TTT
62985 AAGTGTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.45
16 17 0.55
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (16 bp):
TTTTTTTTTTGATTGA
Found at i:70087 original size:30 final size:30
Alignment explanation
Indices: 70052--70114 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
70042 TCAAATTCGA
**
70052 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
70082 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
70112 ATG
1 ATG
70115 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:74543 original size:13 final size:13
Alignment explanation
Indices: 74525--74551 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
74515 ATTGAACGTT
74525 ATAAAAGTAATAA
1 ATAAAAGTAATAA
74538 ATAAAAGTAATAA
1 ATAAAAGTAATAA
74551 A
1 A
74552 ATGAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAAAAGTAATAA
Found at i:74750 original size:18 final size:17
Alignment explanation
Indices: 74724--74765 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
74714 AAGAAAATAT
*
74724 AATAAATAAGTAAAAAC
1 AATAAATAAGTAAAAAA
74741 AATAACATAAGTAAAAAA
1 AATAA-ATAAGTAAAAAA
74759 AATAAAT
1 AATAAAT
74766 TATACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (17 bp):
AATAAATAAGTAAAAAA
Found at i:76233 original size:3 final size:3
Alignment explanation
Indices: 76225--76290 Score: 98
Period size: 3 Copynumber: 21.7 Consensus size: 3
76215 GTATATTGTA
*
76225 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
76271 AAT AAAT AAT AAT AA- AAT AA
1 AAT -AAT AAT AAT AAT AAT AA
76291 ATATAAAAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:77183 original size:13 final size:13
Alignment explanation
Indices: 77167--77199 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
77157 CAGCACCAAA
77167 GACCGACTGCCAT
1 GACCGACTGCCAT
*
77180 GACCGACTGTCAT
1 GACCGACTGCCAT
77193 GACCGAC
1 GACCGAC
77200 CATCACATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.15
Consensus pattern (13 bp):
GACCGACTGCCAT
Found at i:80529 original size:12 final size:12
Alignment explanation
Indices: 80512--80536 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
80502 CTAATGAGGT
80512 TTCTTCTTCTTA
1 TTCTTCTTCTTA
80524 TTCTTCTTCTTA
1 TTCTTCTTCTTA
80536 T
1 T
80537 CGCTCTCTTC
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:0.00, T:0.68
Consensus pattern (12 bp):
TTCTTCTTCTTA
Done.