Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002944.1 Hibiscus syriacus cultivar Beakdansim tig00006076_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: 81769
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:847 original size:22 final size:24
Alignment explanation
Indices: 812--872 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
802 ATTTCATCCC
*
812 TATTAAATTTATATTA-A-TAACTA
1 TATT-AATTAATATTATATTAACTA
*
835 TTTTAATTAATATTATATTAACTA
1 TATTAATTAATATTATATTAACTA
859 TATTAATATAATAT
1 TATTAAT-TAATAT
873 AGTTTATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 10 0.31
23 4 0.12
24 12 0.38
25 6 0.19
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAATTAATATTATATTAACTA
Found at i:927 original size:30 final size:30
Alignment explanation
Indices: 887--1065 Score: 118
Period size: 30 Copynumber: 5.8 Consensus size: 30
877 TATAATTTGT
887 AATT-ATATTAATATAAA-TATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
* *
916 AATTAATATTAATATACACTATTGTTAT-A
1 AATTAATATTAATATAAACTATAGTTATAA
* *
945 AATTATATAGTATAATTTATAAACTATAATTAATAT
1 AATTA-ATA-T-TAA--TATAAACTATAGTT-ATAA
*
981 AATTAATATT-ATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAACTATAG-TTATAA
* * * *
1009 ACTATAACTATATTAATATAAATTATAGTTAGAT
1 A--ATTA--ATATTAATATAAACTATAGTTATAA
*
1043 AATTAACATTAATATAAACTATA
1 AATTAATATTAATATAAACTATA
1066 TAATACATTA
Statistics
Matches: 117, Mismatches: 16, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
28 9 0.08
29 12 0.10
30 40 0.34
31 6 0.05
32 12 0.10
33 5 0.04
34 17 0.15
35 11 0.09
36 5 0.04
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:964 original size:14 final size:14
Alignment explanation
Indices: 941--1007 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
931 ACACTATTGT
*
941 TATAAATTATATAG
1 TATAATTTATATAG
* *
955 TATAATTTATAAAC
1 TATAATTTATATAG
* *
969 TATAATTAATATAA
1 TATAATTTATATAG
983 T-TAATATTATATAG
1 TATAAT-TTATATAG
*
997 TATAGTTTATA
1 TATAATTTATA
1008 AACTATAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
13 4 0.10
14 35 0.83
15 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (14 bp):
TATAATTTATATAG
Found at i:1034 original size:42 final size:42
Alignment explanation
Indices: 941--1035 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
931 ACACTATTGT
*
941 TATAAATTATATAGTATAATTTATAAACTATAATTAATATAA
1 TATAAATTATATAGTATAATTTATAAACTATAACTAATATAA
*
983 T-TAATATTATATAGTATAGTTTATAAACTATAACT-ATATTAA
1 TATAA-ATTATATAGTATAATTTATAAACTATAACTAATA-TAA
1025 TATAAATTATA
1 TATAAATTATA
1036 GTTAGATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
41 6 0.12
42 39 0.81
43 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (42 bp):
TATAAATTATATAGTATAATTTATAAACTATAACTAATATAA
Found at i:1106 original size:21 final size:21
Alignment explanation
Indices: 1077--1129 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1067 AATACATTAA
*
1077 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAT
* **
1098 TATATACTATAGGTTATAAGG
1 TATAAACTATAGGTTATAAAT
1119 TATAAACTATA
1 TATAAACTATA
1130 TAGTACACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAT
Found at i:1252 original size:20 final size:20
Alignment explanation
Indices: 1224--1370 Score: 72
Period size: 20 Copynumber: 7.9 Consensus size: 20
1214 CTAAGGTTTA
* *
1224 TATATATAGTTTATATATAC
1 TATACATAGTTTACATATAC
*
1244 TATACATAGTTTACATACA-
1 TATACATAGTTTACATATAC
1263 TATAC-TA---TA-AGT-TAC
1 TATACATAGTTTACA-TATAC
*
1278 -ATATATAGTTTACATATAC
1 TATACATAGTTTACATATAC
* *
1297 TAT--ATAGTTTATACATAC
1 TATACATAGTTTACATATAC
1315 -ATACTATAAG-TTACATATA-
1 TATAC-AT-AGTTTACATATAC
* *
1334 TATACATA-TATATATATA-
1 TATACATAGTTTACATATAC
*
1352 TATACTATAGGTTACATAT
1 TATAC-ATAGTTTACATAT
1371 TAACTATTGT
Statistics
Matches: 96, Mismatches: 14, Indels: 34
0.67 0.10 0.24
Matches are distributed among these distances:
14 5 0.05
15 5 0.05
17 2 0.02
18 31 0.32
19 14 0.15
20 37 0.39
21 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (20 bp):
TATACATAGTTTACATATAC
Found at i:1266 original size:53 final size:54
Alignment explanation
Indices: 1170--1337 Score: 172
Period size: 53 Copynumber: 3.1 Consensus size: 54
1160 TATAGGTTAC
* *
1170 ATATATAGTTTATATA-AC-ATAAATAGATTGTATATATACATATACTAAGGTTTAT
1 ATATATAGTTTATATATACTATACATAG-TT-TATACATACATATACTAA-GTTTAT
*
1225 ATATATAGTTTATATATACTATACATAG-TT-TACATACATATACTATAAG-TTAC
1 ATATATAGTTTATATATACTATACATAGTTTATACATACATATAC--TAAGTTTAT
* *
1278 ATATATAGTTTACATATACTAT--ATAGTTTATACATACATACTA-TAAGTTACAT
1 ATATATAGTTTATATATACTATACATAGTTTATACATACATA-TACTAAGTT-TAT
1331 ATATATA
1 ATATATA
1338 CATATATATA
Statistics
Matches: 98, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
51 8 0.08
52 3 0.03
53 54 0.55
54 4 0.04
55 20 0.20
56 2 0.02
57 7 0.07
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.42
Consensus pattern (54 bp):
ATATATAGTTTATATATACTATACATAGTTTATACATACATATACTAAGTTTAT
Found at i:1330 original size:38 final size:37
Alignment explanation
Indices: 1275--1370 Score: 99
Period size: 38 Copynumber: 2.6 Consensus size: 37
1265 TACTATAAGT
*
1275 TACATA-TAT-AGTTTACATATACTAT-ATAGTTTATACA
1 TACATACTATAAG-TTACATATA-TATAATA-TATATACA
*
1312 TACATACTATAAGTTACATATATATACATATATATATA
1 TACATACTATAAGTTACATATATATA-ATATATATACA
* *
1350 TATATACTATAGGTTACATAT
1 TACATACTATAAGTTACATAT
1371 TAACTATTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
37 9 0.18
38 37 0.73
39 5 0.10
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (37 bp):
TACATACTATAAGTTACATATATATAATATATATACA
Found at i:1341 original size:10 final size:10
Alignment explanation
Indices: 1326--1355 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1316 TACTATAAGT
1326 TACATATATA
1 TACATATATA
1336 TACATATATA
1 TACATATATA
*
1346 TATATATATA
1 TACATATATA
1356 CTATAGGTTA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TACATATATA
Found at i:1353 original size:51 final size:49
Alignment explanation
Indices: 1158--1351 Score: 142
Period size: 53 Copynumber: 3.7 Consensus size: 49
1148 ATTGTTATAA
* * * * *
1158 ACTATAGGTTACATATATAGTTTATATAACATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTATATAT-ATATATATAG--T-T-TACATACA-AT
* * *
1213 ACTA-AGGTTTATATATATAGTTTATATATACTATACATAGTTTACATACATAT
1 ACTATAAG-TTACATATATAGTATATATATA-TAT--ATAGTTTACATACA-AT
* *
1266 ACTATAAGTTACATATATAGTTTACATATACTATATAGTTTATACATAC-AT
1 ACTATAAGTTACATATATAGTATATATATA-TATATAG-TT-TACATACAAT
*
1317 ACTATAAGTTACATATATA-TACATATATATATATA
1 ACTATAAGTTACATATATAGTATATATATATATATA
1352 TATACTATAG
Statistics
Matches: 122, Mismatches: 10, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
49 6 0.05
50 7 0.06
51 25 0.20
52 2 0.02
53 45 0.37
54 8 0.07
55 25 0.20
57 4 0.03
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (49 bp):
ACTATAAGTTACATATATAGTATATATATATATATAGTTTACATACAAT
Found at i:1370 original size:18 final size:18
Alignment explanation
Indices: 1281--1370 Score: 51
Period size: 18 Copynumber: 4.8 Consensus size: 18
1271 AAGTTACATA
*
1281 TATAGTTTACATATACTA-
1 TATAGGTTACATATA-TAC
* *
1299 TATAGTTTATACATACATAC
1 TATAG-GT-TACATATATAC
*
1319 TATAAGTTACATATATATAC
1 TATAGGTTAC--ATATATAC
*
1339 ATATA--TATATATATATAC
1 -TATAGGT-TACATATATAC
1357 TATAGGTTACATAT
1 TATAGGTTACATAT
1371 TAACTATTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
17 4 0.07
18 22 0.39
19 7 0.12
20 20 0.35
21 4 0.07
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (18 bp):
TATAGGTTACATATATAC
Found at i:1431 original size:14 final size:14
Alignment explanation
Indices: 1412--1460 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
1402 ATAGTTTATA
1412 GTTTAGGAGTTAGG
1 GTTTAGGAGTTAGG
* *
1426 GTTTAGGATTTAGA
1 GTTTAGGAGTTAGG
*
1440 GTTTAGGAGTTAAG
1 GTTTAGGAGTTAGG
1454 GTTTAGG
1 GTTTAGG
1461 GTTTTATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (14 bp):
GTTTAGGAGTTAGG
Found at i:1442 original size:28 final size:27
Alignment explanation
Indices: 1394--1460 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 27
1384 TGCATAGTAT
*
1394 TTAGGGTTATA-GTTTATAGTTTAGGAG
1 TTAGGGTT-TAGGTTTAGAGTTTAGGAG
1421 TTAGGGTTTAGGATTTAGAGTTTAGGAG
1 TTAGGGTTTAGG-TTTAGAGTTTAGGAG
*
1449 TTAAGGTTTAGG
1 TTAGGGTTTAGG
1461 GTTTTATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 2 0.06
27 9 0.25
28 25 0.69
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (27 bp):
TTAGGGTTTAGGTTTAGAGTTTAGGAG
Found at i:1581 original size:23 final size:23
Alignment explanation
Indices: 1562--1695 Score: 66
Period size: 22 Copynumber: 6.0 Consensus size: 23
1552 AAATTATAAT
1562 TTATAAACTATATATTTTATATAG
1 TTATAAA-TATATATTTTATATAG
* *
1586 TTATACATATATA-TATATATTA-
1 TTATAAATATATATTTTATA-TAG
* * * *
1608 ATATAAAT-TATAGTTTATAAAA
1 TTATAAATATATATTTTATATAG
* *
1630 CTAT--ATATATATTTTTTATAG
1 TTATAAATATATATTTTATATAG
* *
1651 TTTATACATAT-TATATATATATAG
1 -TTATAAATATATAT-TTTATATAG
* * *
1675 TT-TATATACATAGTTTATATA
1 TTATAAATATATATTTTATATA
1696 TATAGTTCAT
Statistics
Matches: 83, Mismatches: 18, Indels: 20
0.69 0.15 0.17
Matches are distributed among these distances:
20 2 0.02
21 15 0.18
22 34 0.41
23 15 0.18
24 17 0.20
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (23 bp):
TTATAAATATATATTTTATATAG
Found at i:1584 original size:2 final size:2
Alignment explanation
Indices: 1570--1793 Score: 50
Period size: 2 Copynumber: 115.0 Consensus size: 2
1560 ATTTATAAAC
* *
1570 TA TA TA T- TT TA TA TA GT- TA TA CA TA TA TA TA TA TA T- TA -A
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1609 TA TA AA T- TA TA GTT TA TA -A AA CTA TA TA TA TA T- TT TT TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
1650 GTT TA TA CA TA T- TA TA TA TA TA TA GTT TA TA TA CA TA GTT TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * **
1692 TA TA TA TA GT- TCA TA TA AA CA TA -A T- TA TA TA TA TA GC TA TA
1 TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1733 -A TA -A T- TA TA TA GTT TA TA -A TA TA AA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
1773 AA CT- TA TA T- TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA
1794 AATTATATTT
Statistics
Matches: 160, Mismatches: 34, Indels: 56
0.64 0.14 0.22
Matches are distributed among these distances:
1 17 0.11
2 133 0.83
3 10 0.06
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1600 original size:63 final size:64
Alignment explanation
Indices: 1514--1682 Score: 202
Period size: 60 Copynumber: 2.6 Consensus size: 64
1504 TATAGATTAC
*
1514 TTATATTAGTTATACATACATATATACTATATTAATATAAATTATAATTTAT-AAAC-TATATAT
1 TTATA-TAGTTATACATATATATATA-TATATTAATATAAATTATAATTTATAAAACATATATAT
1577 T
64 T
*
1578 TTATATAGTTATAC--ATATATATATATATTAATATAAATTATAGTTTATAAAACTATATATATA
1 TTATATAGTTATACATATATATATATATATTAATATAAATTATAATTTATAAAAC---ATATATA
1641 TT
63 TT
* *
1643 TTTTATAGTTTATACATATTATATATATATAGTTTATATA
1 TTATATAG-TTATACATA-TATATATATATA-TTAATATA
1683 CATAGTTTAT
Statistics
Matches: 91, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
60 24 0.26
61 12 0.13
63 9 0.10
64 5 0.05
65 15 0.16
66 6 0.07
68 1 0.01
69 12 0.13
70 7 0.08
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (64 bp):
TTATATAGTTATACATATATATATATATATTAATATAAATTATAATTTATAAAACATATATATT
Found at i:1649 original size:30 final size:31
Alignment explanation
Indices: 1570--1672 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 31
1560 ATTTATAAAC
* *
1570 TATATATTTTATATAG-TTATACATA-TATA
1 TATATATTTTTTATAGTTTATACAAACTATA
1599 TATATATTAATATAAATTATAGTTTATA-AAACTATA
1 TATATATT--T-T---TTATAGTTTATACAAACTATA
* *
1635 TATATATTTTTTATAGTTTATACATATTATA
1 TATATATTTTTTATAGTTTATACAAACTATA
1666 TATATAT
1 TATATAT
1673 AGTTTATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
29 8 0.13
30 12 0.20
31 14 0.23
32 1 0.02
33 1 0.02
34 1 0.02
35 7 0.11
36 17 0.28
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (31 bp):
TATATATTTTTTATAGTTTATACAAACTATA
Found at i:1680 original size:13 final size:13
Alignment explanation
Indices: 1631--1708 Score: 78
Period size: 13 Copynumber: 6.5 Consensus size: 13
1621 TTTATAAAAC
1631 TATATATATA-TT
1 TATATATATAGTT
1643 T-T-T-TATAGTT
1 TATATATATAGTT
* *
1653 TATACATAT--TA
1 TATATATATAGTT
1664 TATATATATAGTT
1 TATATATATAGTT
*
1677 TATATACATAGTT
1 TATATATATAGTT
1690 TATATATATAGTT
1 TATATATATAGTT
*
1703 CATATA
1 TATATA
1709 AACATAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
9 4 0.08
10 4 0.08
11 11 0.21
12 1 0.02
13 33 0.62
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:1682 original size:26 final size:26
Alignment explanation
Indices: 1595--1726 Score: 99
Period size: 26 Copynumber: 4.8 Consensus size: 26
1585 GTTATACATA
* *
1595 TATATATATATTAATATAAATTATAGTT
1 TATATACATATT-ATATATA-TATAGTT
* * *
1623 TATAAAACTATATATATATTTTTTATAG-T
1 TAT-ATAC-ATAT-TATA-TATATATAGTT
1652 T-TATACATATTATATATATATAGTT
1 TATATACATATTATATATATATAGTT
1677 TATATACATAGTT-TATATATATAGTT
1 TATATACATA-TTATATATATATAGTT
*
1703 CATATAAACATAATTATATATATA
1 --TATATACAT-ATTATATATATA
1727 GCTATAATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
24 7 0.08
25 6 0.07
26 25 0.30
27 5 0.06
28 14 0.17
29 13 0.15
30 12 0.14
31 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (26 bp):
TATATACATATTATATATATATAGTT
Found at i:1733 original size:18 final size:19
Alignment explanation
Indices: 1712--1768 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 19
1702 TCATATAAAC
1712 ATAATTATATATATAG-CT
1 ATAATTATATATATAGTCT
* *
1730 ATAATAAT-TATATAGTTT
1 ATAATTATATATATAGTCT
* *
1748 ATAA-TATAAATATAGTTT
1 ATAATTATATATATAGTCT
1766 ATA
1 ATA
1769 TATAAACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (19 bp):
ATAATTATATATATAGTCT
Found at i:2140 original size:211 final size:212
Alignment explanation
Indices: 1883--2582 Score: 973
Period size: 211 Copynumber: 3.3 Consensus size: 212
1873 TTCATCCTTT
* *
1883 TGTG-TTGTTTAATTTATTT-AATTTTAATTTGTAGTTTCATATTTGTTCAATTTAGTCCTTAAA
1 TGTGTTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTTAAA
*
1946 ATTATATTTGCATATGAAATTGAC-CATACTTATTACTTATTCTATTTTTTTAATTGGCCCATAA
66 ATTATATTTGCATCTGAAATTGACACATACTTATTACTTATT-TATTTTTTTAATTGGCCCATAA
* *
2010 CTTTTTAAATGGGTATAATTTAGTACTTTT-T-TTAATTTAAACCTCACACTTTAAAATTATTTC
130 CTTTTTAAATGGGTATAATTTAGTACTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
2073 GATTTGATCCCTCATCAA
195 GATTTGATCCCTCATCAA
2091 TGTGTATTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTTAA
1 TGTGT-TTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTTAA
* * * * * *
2156 AAATATATTTGCAGCTGAAATTGACAAATACTTATTACTTATTTATATTTTTAATTGGCCCACAG
65 AATTATATTTGCATCTGAAATTGACACATACTTATTACTTATTTATTTTTTTAATTGGCCCATAA
* *
2221 CTTTTTAAGTGGGTATAATTTAGTACTTTTGTATTAATTTCAACCTTACAATTTAAAATTATTTC
130 CTTTTTAAATGGGTATAATTTAGTACTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
2286 GATTTGAT-CC-C-T---
195 GATTTGATCCCTCATCAA
* * * **
2298 T-TG---GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTTAATTTAGTCCTCCAA
1 TGTGTTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTTAAA
* * * *
2359 ATTATATTTGCATCTGAAATTGACTCATACTTATTATTTATTTATATTCTTTAATTGACCCATAA
66 ATTATATTTGCATCTGAAATTGACACATACTTATTACTTATTTAT-TTTTTTAATTGGCCCATAA
2424 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
130 CTTTTTAAATGGGTATAATTTAGTAC--TTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
* **
2489 TTGATTTGATCATTCATCAA
193 TCGATTTGATCCCTCATCAA
* *
2509 TGTATGTTGTTTAATTTATTTAAA-TTTAATTTGTAATTTCATATTTGTTCAATTTAATTCTTAA
1 TGTGT-TTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTTAA
* *
2573 ATTTGTATTT
65 AATTATATTT
2583 TTCATAAAAT
Statistics
Matches: 430, Mismatches: 42, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
202 93 0.22
203 39 0.09
205 45 0.10
206 2 0.00
207 2 0.00
208 5 0.01
210 16 0.04
211 113 0.26
212 20 0.05
213 37 0.09
215 42 0.10
216 16 0.04
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (212 bp):
TGTGTTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTTAAA
ATTATATTTGCATCTGAAATTGACACATACTTATTACTTATTTATTTTTTTAATTGGCCCATAAC
TTTTTAAATGGGTATAATTTAGTACTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCG
ATTTGATCCCTCATCAA
Found at i:14837 original size:19 final size:19
Alignment explanation
Indices: 14813--14864 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
14803 TTTGTTTCAC
14813 GTAATTCATTTTCCGGAAT
1 GTAATTCATTTTCCGGAAT
14832 GTAATTCATTTTCCGGAAT
1 GTAATTCATTTTCCGGAAT
14851 GTAATTCATTTTCC
1 GTAATTCATTTTCC
14865 TAATAACCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (19 bp):
GTAATTCATTTTCCGGAAT
Found at i:15091 original size:21 final size:23
Alignment explanation
Indices: 15038--15099 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
15028 TATTTATAAA
*
15038 AATA-TTTAA-AATATATTTATT
1 AATATTTTAATAATATATATATT
15059 AATATTTATAATAATATA-ATATT
1 AATATTT-TAATAATATATATATT
*
15082 -ATATTTTAATATTATATA
1 AATATTTTAATAATATATA
15100 AAATAATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 13 0.37
22 9 0.26
23 7 0.20
24 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTTAATAATATATATATT
Found at i:15157 original size:22 final size:22
Alignment explanation
Indices: 15127--15208 Score: 56
Period size: 25 Copynumber: 3.3 Consensus size: 22
15117 ATAATATAAT
*
15127 ATAAGATATTATTTTTATTTTA
1 ATAATATATTATTTTTATTTTA
15149 ATAATATATAATAATTTTTATATATTTA
1 ATAATATAT--T-A-TTTT-TAT-TTTA
* *
15177 ATAATAATATTATATATATATTTAA
1 ATAAT-ATATTAT-T-TTTATTTTA
15202 ATAATAT
1 ATAATAT
15209 TTTAGTAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 8 0.17
24 3 0.06
25 10 0.21
26 9 0.19
27 5 0.10
28 9 0.19
29 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
ATAATATATTATTTTTATTTTA
Found at i:15183 original size:24 final size:24
Alignment explanation
Indices: 15156--15207 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
15146 TTAATAATAT
15156 ATAATAAT-TT-T-TATATATTTA
1 ATAATAATATTATATATATATTTA
15177 ATAATAATATTATATATATATTTAA
1 ATAATAATATTATATATATATTT-A
15202 ATAATA
1 ATAATA
15208 TTTTAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.30
22 2 0.07
23 1 0.04
24 9 0.33
25 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATAATATTATATATATATTTA
Found at i:15372 original size:90 final size:86
Alignment explanation
Indices: 15224--15391 Score: 196
Period size: 90 Copynumber: 1.9 Consensus size: 86
15214 TAAAGATATT
* * * * * *
15224 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAA-A
15289 TAATTTATAATATTTTATTTCAC
65 TAATTT-TAATATTTTATTTCAC
*
15312 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATA-TTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
15375 AAATTATTTTAATATTT
62 AAATAATTTTAATATTT
15392 AAAATAATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
88 17 0.25
89 8 0.12
90 21 0.31
91 12 0.18
92 10 0.15
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:18867 original size:44 final size:44
Alignment explanation
Indices: 18805--18888 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
18795 ATTTTATCCC
* * *
18805 AAAAATACTGCTCAATGTTCTGACATATAGTGACGTTTGTTCTA
1 AAAAATACTGCTAAATGTTATGACATATAGTGACATTTGTTCTA
*
18849 AAAAATA-TCGCTAAATGTTATGTCATATAGTGACATTTGT
1 AAAAATACT-GCTAAATGTTATGACATATAGTGACATTTGT
18889 AAATGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (44 bp):
AAAAATACTGCTAAATGTTATGACATATAGTGACATTTGTTCTA
Found at i:19118 original size:21 final size:21
Alignment explanation
Indices: 19094--19152 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
19084 ATTATCCAAT
*
19094 AAACTTGATATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
19115 AAACTTGAAATACATAACAAG
1 AAACTTGAAATCCATAACAAC
19136 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
19153 TAATAAATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:22088 original size:40 final size:41
Alignment explanation
Indices: 22041--22158 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 41
22031 TACAAACGTC
*
22041 ACTAAAGTA-TAATATTTAGCGATGTTTATATAAAAACGCT
1 ACTAAAGTACGAATATTTAGCGATGTTTATATAAAAACGCT
* * * *
22081 ACTAAAGTACGAGTATTTAGCGGTGTTTATATAAAAATGCC
1 ACTAAAGTACGAATATTTAGCGATGTTTATATAAAAACGCT
* * * * ** *
22122 CCTAAAGAACGAGTATTTACCGACATTTATTTAAAAA
1 ACTAAAGTACGAATATTTAGCGATGTTTATATAAAAA
22159 ACACCGCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
40 9 0.14
41 56 0.86
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (41 bp):
ACTAAAGTACGAATATTTAGCGATGTTTATATAAAAACGCT
Found at i:22108 original size:41 final size:41
Alignment explanation
Indices: 22053--22158 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
22043 TAAAGTATAA
* *
22053 TATTTAGCGATGTTTATATAAAAACGCTACTAAAGTACGAG
1 TATTTAGCGATGTTTATATAAAAACGCCACTAAAGAACGAG
* * *
22094 TATTTAGCGGTGTTTATATAAAAATGCCCCTAAAGAACGAG
1 TATTTAGCGATGTTTATATAAAAACGCCACTAAAGAACGAG
* ** *
22135 TATTTACCGACATTTATTTAAAAA
1 TATTTAGCGATGTTTATATAAAAA
22159 ACACCGCTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (41 bp):
TATTTAGCGATGTTTATATAAAAACGCCACTAAAGAACGAG
Found at i:36210 original size:136 final size:138
Alignment explanation
Indices: 35964--36236 Score: 451
Period size: 136 Copynumber: 2.0 Consensus size: 138
35954 ATCATATATT
* *
35964 TTTAAGAGGATTAACAAAAATATTTATATAGATAATTCATCAACAAATATTATTCGTGCGGTTTG
1 TTTAAGAGGATTAACAAAAATATTTATACAGATAATTCACCAACAAATATTATTCGTGCGGTTTG
* * *
36029 TATTAGGATTATACTGAGCGAGAGACAGTCGTCCTTTTAAAATTTTGAATTCTATTATGATTTAA
66 TATTAGGATTATACCGAGCGAGAGACAGTCGTCCCTTTAAAATTTTGAATTCTACTATGATTTAA
36094 ATTTTTTC
131 ATTTTTTC
*
36102 TTTAAGAGGATTAACAAAAATA-TT-TACAGATAATTCACCAACAGATATTATTCGTGCGGTTTG
1 TTTAAGAGGATTAACAAAAATATTTATACAGATAATTCACCAACAAATATTATTCGTGCGGTTTG
* * *
36165 TATTAGGATTGTACCGAGGGAGAGACAGTCGTCCCTTTAAAATTTTGAATTCTACTATGATTTAG
66 TATTAGGATTATACCGAGCGAGAGACAGTCGTCCCTTTAAAATTTTGAATTCTACTATGATTTAA
36230 ATTTTTT
131 ATTTTTT
36237 AAAGACAAGA
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
136 102 0.81
137 2 0.02
138 22 0.17
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (138 bp):
TTTAAGAGGATTAACAAAAATATTTATACAGATAATTCACCAACAAATATTATTCGTGCGGTTTG
TATTAGGATTATACCGAGCGAGAGACAGTCGTCCCTTTAAAATTTTGAATTCTACTATGATTTAA
ATTTTTTC
Found at i:38613 original size:2 final size:2
Alignment explanation
Indices: 38608--38633 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38598 TTATTTCTCA
38608 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
38634 TTGCAGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44848 original size:44 final size:44
Alignment explanation
Indices: 44799--44925 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 44
44789 TTAAACATTA
44799 TATTTTATCATTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCATTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
44843 TATTTTA--ATTAAGTTTTAGG-A---TA--TT--AT---TTTTA-
1 TATTTTATCATT--GTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
*
44875 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCATTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
44919 TATTTTA
1 TATTTTA
44926 ATTAGGATTT
Statistics
Matches: 66, Mismatches: 1, Indels: 32
0.67 0.01 0.32
Matches are distributed among these distances:
32 15 0.23
33 6 0.09
34 2 0.03
36 4 0.06
38 4 0.06
40 4 0.06
42 3 0.05
43 6 0.09
44 22 0.33
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (44 bp):
TATTTTATCATTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
Found at i:44903 original size:76 final size:75
Alignment explanation
Indices: 44796--45011 Score: 317
Period size: 76 Copynumber: 2.9 Consensus size: 75
44786 ATTTTAAACA
* *
44796 TTATATTTTATCATTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
*
44861 GGATATTATTT
66 GAATATTA-TT
*
44872 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
*
44937 TAATATTATT
66 GAATATTATT
* * * * *
44947 TTAAATATTATTTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTT
45011 A
65 A
45012 AGATGTTTTA
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
74 5 0.04
75 57 0.44
76 68 0.52
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GAATATTATT
Found at i:45657 original size:16 final size:16
Alignment explanation
Indices: 45612--45659 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
45602 ATTTATCCCA
45612 ATTTAGTTATTTTATTT
1 ATTTA-TTATTTTATTT
45629 ATTTATT-TGTTTATTT
1 ATTTATTAT-TTTATTT
45645 AATTT-TTATTTTATT
1 -ATTTATTATTTTATT
45660 ATACTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 17 0.61
17 10 0.36
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (16 bp):
ATTTATTATTTTATTT
Found at i:45827 original size:22 final size:22
Alignment explanation
Indices: 45785--45827 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
45775 GGAATTCTAT
* *
45785 ATTTTCCTAAAATCAAGAAACA
1 ATTTTACTAAAATCAAAAAACA
45807 ATTTTACT-AAATCACAAAAAC
1 ATTTTACTAAAATCA-AAAAAC
45828 CATAGTCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (22 bp):
ATTTTACTAAAATCAAAAAACA
Found at i:48064 original size:64 final size:65
Alignment explanation
Indices: 47977--48120 Score: 204
Period size: 64 Copynumber: 2.2 Consensus size: 65
47967 AATTGTTCAA
* *
47977 TGTGTATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAAAAATGGAAACATCGAATGCAAT
1 TGTGTATCGATGCATAAGGAAGTGCATCGATACACCCCATT-AAAATGAAAACATCGAATGCAAT
48040 T
65 T
* * **
48041 TGTGCATCGATGCATAAGG-AGTGCATCGATACACCCCCTTAAAATGAAAACATCGAATGTGATT
1 TGTGTATCGATGCATAAGGAAGTGCATCGATACACCCCATTAAAATGAAAACATCGAATGCAATT
48105 TGTGTATCGATGCATA
1 TGTGTATCGATGCATA
48121 TGTTAAAGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
64 63 0.89
65 8 0.11
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (65 bp):
TGTGTATCGATGCATAAGGAAGTGCATCGATACACCCCATTAAAATGAAAACATCGAATGCAATT
Found at i:48152 original size:20 final size:20
Alignment explanation
Indices: 48127--48164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48117 CATATGTTAA
48127 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
* *
48147 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
48165 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:48479 original size:17 final size:16
Alignment explanation
Indices: 48457--48496 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
48447 TAATATTAAA
48457 TGTATGTATACATGAAT
1 TGTATGTATACATG-AT
**
48474 TGTATGTATGTATGAT
1 TGTATGTATACATGAT
48490 TGTATGT
1 TGTATGT
48497 GTTAACATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (16 bp):
TGTATGTATACATGAT
Found at i:49377 original size:29 final size:27
Alignment explanation
Indices: 49304--49545 Score: 250
Period size: 29 Copynumber: 8.6 Consensus size: 27
49294 GTTATGGTGG
* * * *
49304 TATTTTCGTAAATATTGTTAAGAAGGTGT
1 TATTTTGGTAATTATT-TTAA-AAAGTGA
* * *
49333 TAGTTTCGTAAATATTGTTAAACAAGTGA
1 TATTTTGGTAATTATT-TTAAA-AAGTGA
* *
49362 TATTTTGTTAATTATTTCAAAAAAGTGA
1 TATTTTGGTAATTATTT-TAAAAAGTGA
49390 TATTTTGGTAATTATTTTAAAAAAAGTGA
1 TATTTTGGTAATTATTTT--AAAAAGTGA
*
49419 TATTTTGGTAATTATTTCAAAAAGTGA
1 TATTTTGGTAATTATTTTAAAAAGTGA
49446 TATTTTGGTAATTATTTTGAAAAAGTGA
1 TATTTTGGTAATTATTTT-AAAAAGTGA
* *
49474 TATTTTGGTAATTATTTGGAAAAGGTTGA
1 TATTTTGGTAATTATTT-TAAAAAG-TGA
**
49503 TATTTTGGTAATTATTTCGAAAAGTTGA
1 TATTTTGGTAATTATTTTAAAAAG-TGA
*
49531 TATTTTCGTAATTAT
1 TATTTTGGTAATTAT
49546 AAAAAAATAT
Statistics
Matches: 188, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
27 26 0.14
28 77 0.41
29 85 0.45
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (27 bp):
TATTTTGGTAATTATTTTAAAAAGTGA
Found at i:49388 original size:28 final size:27
Alignment explanation
Indices: 49356--49545 Score: 254
Period size: 28 Copynumber: 6.8 Consensus size: 27
49346 ATTGTTAAAC
*
49356 AAGTGATATTTTGTTAATTATTTCAAAA
1 AAGTGATATTTTGGTAATTATTTC-AAA
*
49384 AAGTGATATTTTGGTAATTATTTTAAAAA
1 AAGTGATATTTTGGTAATTA-TTT-CAAA
49413 AAGTGATATTTTGGTAATTATTTCAAA
1 AAGTGATATTTTGGTAATTATTTCAAA
*
49440 AAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTA-TTTCAAA
*
49468 AAGTGATATTTTGGTAATTATTTGGAAA
1 AAGTGATATTTTGGTAATTATTT-CAAA
* *
49496 AGGTTGATATTTTGGTAATTATTTCGAA
1 AAG-TGATATTTTGGTAATTATTTCAAA
*
49524 AAGTTGATATTTTCGTAATTAT
1 AAG-TGATATTTTGGTAATTAT
49546 AAAAAAATAT
Statistics
Matches: 148, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
27 26 0.18
28 76 0.51
29 46 0.31
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (27 bp):
AAGTGATATTTTGGTAATTATTTCAAA
Found at i:49525 original size:57 final size:55
Alignment explanation
Indices: 49356--49545 Score: 256
Period size: 57 Copynumber: 3.4 Consensus size: 55
49346 ATTGTTAAAC
* *
49356 AAGTGATATTTTGTTAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTTAAAAA
1 AAGTGATATTTTGGTAATTATTT-AAAAAAGTGATATTTTGGTAATTA-TTTAGAAA
* *
49413 AAGTGATATTTTGGTAATTATTTCAAAAAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTAAAAAAGTGATATTTTGGTAATTATTTAGAAA
* * *
49468 AAGTGATATTTTGGTAATTATTTGGAAAAGGTTGATATTTTGGTAATTATTTCG-AA
1 AAGTGATATTTTGGTAATTATTT-AAAAAAG-TGATATTTTGGTAATTATTTAGAAA
*
49524 AAGTTGATATTTTCGTAATTAT
1 AAG-TGATATTTTGGTAATTAT
49546 AAAAAAATAT
Statistics
Matches: 122, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
55 29 0.24
56 33 0.27
57 60 0.49
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (55 bp):
AAGTGATATTTTGGTAATTATTTAAAAAAGTGATATTTTGGTAATTATTTAGAAA
Found at i:50605 original size:31 final size:32
Alignment explanation
Indices: 50560--50629 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
50550 TGAGTCGAGC
* * *
50560 CTTGGGT-AGGCTTTGTGGCCCTGAG-ATTTT
1 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTGT
50590 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTGT
1 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTGT
50622 CTTGGGTA
1 CTTGGGTA
50630 GGCTCGCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 7 0.20
31 16 0.46
32 12 0.34
ACGTcount: A:0.13, C:0.19, G:0.33, T:0.36
Consensus pattern (32 bp):
CTTGGGTAAGCCTTTGTGGCCCCGAGAATTGT
Found at i:51534 original size:25 final size:25
Alignment explanation
Indices: 51506--51557 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
51496 CGCAGCGGAG
51506 TGGCTAGTTTTACAGACCTGGTAGA
1 TGGCTAGTTTTACAGACCTGGTAGA
51531 TGGCTAGTTTTACAGACCTGGTAGA
1 TGGCTAGTTTTACAGACCTGGTAGA
51556 TG
1 TG
51558 AGATACGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (25 bp):
TGGCTAGTTTTACAGACCTGGTAGA
Found at i:53716 original size:28 final size:28
Alignment explanation
Indices: 53684--53872 Score: 292
Period size: 28 Copynumber: 6.8 Consensus size: 28
53674 ATTGTTAAAC
* *
53684 AAGTGATATTTTGTTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
*
53712 AAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
53740 AAGTGATATTTTGGTAATTATTTCG-AA
1 AAGTGATATTTTGGTAATTATTTCGAAA
*
53767 AAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
53795 AAGTGATATTTTGGTAATTATTTCGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
*
53823 AGGTTGATATTTTGGTAATTATTTCG-AA
1 AAG-TGATATTTTGGTAATTATTTCGAAA
*
53851 AAGTTGATATTTTCGTAATTAT
1 AAG-TGATATTTTGGTAATTAT
53873 AAAAAAATGT
Statistics
Matches: 152, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
27 26 0.17
28 104 0.68
29 22 0.14
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (28 bp):
AAGTGATATTTTGGTAATTATTTCGAAA
Found at i:53778 original size:83 final size:83
Alignment explanation
Indices: 53684--53872 Score: 317
Period size: 83 Copynumber: 2.2 Consensus size: 83
53674 ATTGTTAAAC
*
53684 AAGTGATATTTTGTTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAAAAG-TGATA
1 AAGTGATATTTTG-TAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAGTTGATA
53748 TTTTGGTAATTATTTCGAA
65 TTTTGGTAATTATTTCGAA
*
53767 AAGTGATATTTTGGTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTCGAAAAGGTTGATA
1 AAGTGATATTTT-GTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAGTTGATA
53832 TTTTGGTAATTATTTCGAA
65 TTTTGGTAATTATTTCGAA
53851 AAGTTGATATTTTCGTAATTAT
1 AAG-TGATATTTT-GTAATTAT
53873 AAAAAAATGT
Statistics
Matches: 100, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
83 55 0.55
84 28 0.28
85 17 0.17
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (83 bp):
AAGTGATATTTTGTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAGTTGATAT
TTTGGTAATTATTTCGAA
Found at i:53791 original size:55 final size:55
Alignment explanation
Indices: 53684--53872 Score: 299
Period size: 55 Copynumber: 3.4 Consensus size: 55
53674 ATTGTTAAAC
* *
53684 AAGTGATATTTTGTTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTCG-AAAAGTGATATTTTGGTAATTATTTTGAAA
53740 AAGTGATATTTTGGTAATTATTTCGAAAAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAAAGTGATATTTTGGTAATTATTTTGAAA
*
53795 AAGTGATATTTTGGTAATTATTTCGAAAAGGTTGATATTTTGGTAATTATTTCG-AA
1 AAGTGATATTTTGGTAATTATTTCGAAAA-G-TGATATTTTGGTAATTATTTTGAAA
*
53851 AAGTTGATATTTTCGTAATTAT
1 AAG-TGATATTTTGGTAATTAT
53873 AAAAAAATGT
Statistics
Matches: 126, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
55 59 0.47
56 29 0.23
57 38 0.30
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (55 bp):
AAGTGATATTTTGGTAATTATTTCGAAAAGTGATATTTTGGTAATTATTTTGAAA
Found at i:54932 original size:31 final size:32
Alignment explanation
Indices: 54887--54956 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
54877 TGAGTCGAGC
* * *
54887 CTTGGGT-AGGCTTTGCGGCCCTGAG-ATTTT
1 CTTGGGTAAGCCTTTGCGGCCCCGAGAATTGT
*
54917 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTGT
1 CTTGGGTAAGCCTTTGCGGCCCCGAGAATTGT
54949 CTTGGGTA
1 CTTGGGTA
54957 GGCTCGCAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 7 0.21
31 15 0.44
32 12 0.35
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.34
Consensus pattern (32 bp):
CTTGGGTAAGCCTTTGCGGCCCCGAGAATTGT
Found at i:55679 original size:32 final size:31
Alignment explanation
Indices: 55638--55762 Score: 105
Period size: 31 Copynumber: 4.0 Consensus size: 31
55628 AGTTGAGGGT
*
55638 TTACCTATGTTATACGGAATATATGGACA-TAA
1 TTACCTATGTT-TACGGAACATATGGACAGT-A
*
55670 TTACCTATGTCTTTC-GAGACATATGGACAGTA
1 TTACCTATGT-TTACGGA-ACATATGGACAGTA
*
55702 -TACCTATGTTCTAAGGAACATATGGACAGT-
1 TTACCTATGTT-TACGGAACATATGGACAGTA
* * * *
55732 TTACCTAGGTTCTTCGGGACCTATGGACAGT
1 TTACCTATGTT-TACGGAACATATGGACAGT
55763 TACCGAGGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
30 1 0.01
31 50 0.64
32 25 0.32
33 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTTACGGAACATATGGACAGTA
Found at i:55783 original size:30 final size:31
Alignment explanation
Indices: 55691--55775 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
55681 TTTCGAGACA
* * * * *
55691 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGTTTACCGAGGTTCTTCAGG-ACC
* *
55722 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAGTTTACCGAGGTTCTTCAGGACC
55753 TATGGACAG-TTACCGAGGTTCTT
1 TATGGACAGTTTACCGAGGTTCTT
55776 TATGACCTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 13 0.28
31 31 0.66
32 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTCAGGACC
Found at i:59284 original size:20 final size:20
Alignment explanation
Indices: 59259--59296 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59249 CACATGTTAA
59259 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
* *
59279 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
59297 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:59611 original size:17 final size:16
Alignment explanation
Indices: 59589--59628 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
59579 TAATATTAAA
59589 TGTATGTATACATGAAT
1 TGTATGTATACATG-AT
**
59606 TGTATGTATGTATGAT
1 TGTATGTATACATGAT
59622 TGTATGT
1 TGTATGT
59629 GTTAACATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (16 bp):
TGTATGTATACATGAT
Found at i:59896 original size:32 final size:31
Alignment explanation
Indices: 59855--59955 Score: 111
Period size: 31 Copynumber: 3.2 Consensus size: 31
59845 AGTCGAGGGT
59855 TTACCTATGTTATACGGAACATATGGACA-TAA
1 TTACCTATGTT-TACGGAACATATGGACAGT-A
*
59887 TTACCTATGTCTTTC-GAGACATATGGACAGTA
1 TTACCTATGT-TTACGGA-ACATATGGACAGTA
*
59919 -TACCTATGTTCTAAGGAACATATGGACAGT-
1 TTACCTATGTT-TACGGAACATATGGACAGTA
59949 TTACCTA
1 TTACCTA
59956 GGTTCTTCGG
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
30 1 0.02
31 31 0.52
32 26 0.43
33 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTTACGGAACATATGGACAGTA
Found at i:64962 original size:20 final size:20
Alignment explanation
Indices: 64903--64971 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
64893 TTCGTTATTT
*
64903 TTTTGTTTTATTTTCAGTGAA
1 TTTTATTTTATTTTCAGT-AA
*
64924 TTTTATTTCA--TT-A-T-A
1 TTTTATTTTATTTTCAGTAA
64939 -TTTATTTTATTTTCAGTAA
1 TTTTATTTTATTTTCAGTAA
64958 TTTTATTTTATTTT
1 TTTTATTTTATTTT
64972 TCTCTAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.21
15 1 0.03
16 2 0.05
17 2 0.05
18 2 0.05
19 3 0.08
20 13 0.33
21 8 0.21
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (20 bp):
TTTTATTTTATTTTCAGTAA
Found at i:66307 original size:29 final size:28
Alignment explanation
Indices: 66251--66307 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
66241 TCAAATTTAG
* * **
66251 TTATTTTATTTATTTGTTTATTTAATTT
1 TTATTTTATTTACTTCTTTAAATAATTT
66279 TTATTTTATTATACTTCTTTAAATAATTT
1 TTATTTTATT-TACTTCTTTAAATAATTT
66308 AAAATCCTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (28 bp):
TTATTTTATTTACTTCTTTAAATAATTT
Found at i:71665 original size:24 final size:24
Alignment explanation
Indices: 71638--71688 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
71628 ATAATCAAGT
71638 TCAAGTATCAGATCAAAATCCAGG
1 TCAAGTATCAGATCAAAATCCAGG
*
71662 TCAAGTATCCGATCAAAATCCAGG
1 TCAAGTATCAGATCAAAATCCAGG
71686 TCA
1 TCA
71689 GGAATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.22
Consensus pattern (24 bp):
TCAAGTATCAGATCAAAATCCAGG
Found at i:77467 original size:74 final size:75
Alignment explanation
Indices: 77371--77578 Score: 260
Period size: 74 Copynumber: 2.8 Consensus size: 75
77361 ACATTATATT
* * *
77371 TTATCTTTG-TTTAAGGTTTTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATAT
1 TTATCTTTGTTTTAA-GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATAT
*
77435 TATTTT-TATA
65 TATTTTAAATA
* * *
77445 TTCTCTTTGTTTTAAGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTATAATATT
1 TTATCTTTGTTTTAAGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
77510 ATTTTAAATA
66 ATTTTAAATA
* * * * *
77520 TTATTTTTGTTTTAGGTATTTTTAGTTTAAATA-GTTTTAAATGTTTTAATTAGGATTTA
1 TTATCTTTGTTTTAAGTA-TTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTTA
77579 AGATGTTTTA
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
74 58 0.49
75 28 0.24
76 32 0.27
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (75 bp):
TTATCTTTGTTTTAAGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATT
ATTTTAAATA
Found at i:78199 original size:17 final size:17
Alignment explanation
Indices: 78174--78216 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
78164 CTTTATCCCA
*
78174 ATTTAATTATTTTATTT
1 ATTTAATTATTTAATTT
*
78191 ATTTGATTATTTAATTT
1 ATTTAATTATTTAATTT
*
78208 -TTTTATTAT
1 ATTTAATTAT
78217 ACTACTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTAATTATTTAATTT
Found at i:79440 original size:25 final size:27
Alignment explanation
Indices: 79374--79450 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 27
79364 ATAACATCAA
*
79374 TAATTTTAAAATATAAAATATTACTCTTT
1 TAATTATAAAA-A-AAAATATTACTCTTT
**
79403 TAATTATCCAAAAAAATATTACT-TTT
1 TAATTATAAAAAAAAATATTACTCTTT
*
79429 TTA-TATAAAAAAACTAATATTA
1 TAATTATAAAAAAA--AATATTA
79451 AACATTGAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
25 8 0.20
26 5 0.12
27 18 0.45
28 1 0.03
29 8 0.20
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATTATAAAAAAAAATATTACTCTTT
Found at i:79686 original size:22 final size:22
Alignment explanation
Indices: 79652--79699 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
79642 TATTCAATCC
*
79652 AAAAAAATCTTTAAAATATATT
1 AAAAAAATATTTAAAATATATT
* * *
79674 AAAAAATTATTTAATATATGTT
1 AAAAAAATATTTAAAATATATT
79696 AAAA
1 AAAA
79700 GACATTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAAATATTTAAAATATATT
Found at i:79822 original size:19 final size:18
Alignment explanation
Indices: 79797--79840 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
79787 TTAAATTAGT
* *
79797 TAATTTTTTTAATTTATC
1 TAATTTTCTAAATTTATC
*
79815 TAAATTTTCTAAATTTTTC
1 T-AATTTTCTAAATTTATC
79834 TAATTTT
1 TAATTTT
79841 AATAATTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTTTCTAAATTTATC
Done.