Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016092.1 Corchorus capsularis cultivar CVL-1 contig16113, 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: 73748
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:279 original size:32 final size:33
Alignment explanation
Indices: 224--287 Score: 103
Period size: 35 Copynumber: 1.9 Consensus size: 33
214 AAGTTTTGAT
224 TTCCTCAAGGAAGAAGAATAAGAAAATTGCAGGAC
1 TTCCTCAAGGAAGAAG-A-AAGAAAATTGCAGGAC
259 TTCCTCAAGGAAGAAG-AAGAAAATTGCAG
1 TTCCTCAAGGAAGAAGAAAGAAAATTGCAG
288 AACCTCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 13 0.45
35 16 0.55
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.17
Consensus pattern (33 bp):
TTCCTCAAGGAAGAAGAAAGAAAATTGCAGGAC
Found at i:1032 original size:22 final size:22
Alignment explanation
Indices: 1014--1510 Score: 203
Period size: 22 Copynumber: 23.4 Consensus size: 22
1004 CAATTACCAC
1014 TTACTGATTACTATTTTACTCT
1 TTACTGATTACTATTTTACTCT
1036 TTACTGATTACTATTTTACTCT
1 TTACTGATTACTATTTTACTCT
*
1058 TTACTGATTACT-CTTTACTCT
1 TTACTGATTACTATTTTACTCT
* *
1079 TTACTGATTAATATTTTATTCT
1 TTACTGATTACTATTTTACTCT
* * *
1101 TTACTGATTGC--CTTTACTTT
1 TTACTGATTACTATTTTACTCT
*
1121 TTACTGATTAATATTTTACTCT
1 TTACTGATTACTATTTTACTCT
* * * ** **
1143 CTAC-CATT-TTCCTTTACTGA
1 TTACTGATTACTATTTTACTCT
** **
1163 TTACTCTTTA-TCCTTTAC-CATT
1 TTACTGATTACTATTTTACTC--T
* * *
1185 TTACTGATTTCT-TCTCACT-T
1 TTACTGATTACTATTTTACTCT
*
1205 CTTACT-ATT--T-TTTT-TTCT
1 -TTACTGATTACTATTTTACTCT
1223 TTACTGATTACTTTTTACTCTTTACTCT
1 TTACTGATTAC----TA-T-TTTACTCT
* * *
1251 TTACTTATTACT-CTTTACTTT
1 TTACTGATTACTATTTTACTCT
* *
1272 TTACTAATTACCATTTTACT-T
1 TTACTGATTACTATTTTACTCT
* ** **
1293 TAAACTGATTACCCTTTTACAAT
1 T-TACTGATTACTATTTTACTCT
* * *
1316 TTTCTAATTACCATTTTACT-T
1 TTACTGATTACTATTTTACTCT
*
1337 TTCACTGATTAC--TTTTACTTT
1 TT-ACTGATTACTATTTTACTCT
* *
1358 TTACTGATTACCATTTTACTTT
1 TTACTGATTACTATTTTACTCT
* * *
1380 TTATTAATTACCT-TTTTACTTT
1 TTACTGATTA-CTATTTTACTCT
* *
1402 TTACTGATTGCCA--TTACT-T
1 TTACTGATTACTATTTTACTCT
1421 CTTACTGA-T-C-ATTATTACTCT
1 -TTACTGATTACTATT-TTACTCT
*
1442 TTACTGATTACCATATTT--TCT
1 TTACTGATTACTAT-TTTACTCT
1463 TTACTGATTACT-TTTTA--CT
1 TTACTGATTACTATTTTACTCT
** * *
1482 TTACTCTTTACCATTTT-CTTT
1 TTACTGATTACTATTTTACTCT
1503 TTACTGAT
1 TTACTGAT
1511 CTCTCTTTAC
Statistics
Matches: 366, Mismatches: 65, Indels: 89
0.70 0.12 0.17
Matches are distributed among these distances:
17 7 0.02
18 8 0.02
19 16 0.04
20 74 0.20
21 87 0.24
22 146 0.40
23 8 0.02
24 3 0.01
26 1 0.00
27 3 0.01
28 13 0.04
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.55
Consensus pattern (22 bp):
TTACTGATTACTATTTTACTCT
Found at i:1038 original size:7 final size:7
Alignment explanation
Indices: 1028--1083 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
1018 TGATTACTAT
1028 TTTACTC
1 TTTACTC
*
1035 TTTACTG
1 TTTACTC
* *
1042 ATTACTAT
1 TTTACT-C
1050 TTTACTC
1 TTTACTC
*
1057 TTTACTG
1 TTTACTC
*
1064 ATTACTC
1 TTTACTC
1071 TTTACTC
1 TTTACTC
1078 TTTACT
1 TTTACT
1084 GATTAATATT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 34 0.87
8 5 0.13
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (7 bp):
TTTACTC
Found at i:1082 original size:43 final size:43
Alignment explanation
Indices: 1014--1142 Score: 197
Period size: 43 Copynumber: 3.0 Consensus size: 43
1004 CAATTACCAC
* *
1014 TTACTGATTACTATTTTACTCTTTACTGATTACTATTTTACTCT
1 TTACTGATTACT-CTTTACTCTTTACTGATTAATATTTTACTCT
*
1058 TTACTGATTACTCTTTACTCTTTACTGATTAATATTTTATTCT
1 TTACTGATTACTCTTTACTCTTTACTGATTAATATTTTACTCT
* *
1101 TTACTGATTGC-CTTTACTTTTTACTGATTAATATTTTACTCT
1 TTACTGATTACTCTTTACTCTTTACTGATTAATATTTTACTCT
1143 CTACCATTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 29 0.37
43 38 0.48
44 12 0.15
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.55
Consensus pattern (43 bp):
TTACTGATTACTCTTTACTCTTTACTGATTAATATTTTACTCT
Found at i:1240 original size:7 final size:7
Alignment explanation
Indices: 1230--1406 Score: 63
Period size: 7 Copynumber: 24.7 Consensus size: 7
1220 TCTTTACTGA
1230 TTACTTT
1 TTACTTT
*
1237 TTACTCT
1 TTACTTT
*
1244 TTACTCT
1 TTACTTT
*
1251 TTACTTA
1 TTACTTT
*
1258 TTACTCT
1 TTACTTT
1265 TTACTTT
1 TTACTTT
**
1272 TTACTAA
1 TTACTTT
*
1279 TTACCATT
1 TTA-CTTT
1287 TTACTTT
1 TTACTTT
** **
1294 AAACTGA
1 TTACTTT
*
1301 TTACCCTT
1 TTA-CTTT
*
1309 TTACAATT
1 TTAC-TTT
**
1317 TT-CTAA
1 TTACTTT
*
1323 TTACCATT
1 TTA-CTTT
1331 TTACTTT
1 TTACTTT
* **
1338 TCACTGA
1 TTACTTT
1345 TTAC-TT
1 TTACTTT
1351 TTACTTT
1 TTACTTT
**
1358 TTACTGA
1 TTACTTT
*
1365 TTACCATT
1 TTA-CTTT
1373 TTACTTT
1 TTACTTT
*
1380 TTA-TTAA
1 TTACTT-T
1387 TTACCTTT
1 TTA-CTTT
1395 TTACTTT
1 TTACTTT
1402 TTACT
1 TTACT
1407 GATTGCCATT
Statistics
Matches: 117, Mismatches: 43, Indels: 20
0.65 0.24 0.11
Matches are distributed among these distances:
6 8 0.07
7 84 0.72
8 23 0.20
9 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.02, T:0.56
Consensus pattern (7 bp):
TTACTTT
Found at i:1270 original size:14 final size:14
Alignment explanation
Indices: 1220--1276 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
1210 TATTTTTTTT
*
1220 TCTTTACTGATTAC
1 TCTTTACTTATTAC
*
1234 TTTTTACTCT-TTAC
1 TCTTTACT-TATTAC
1248 TCTTTACTTATTAC
1 TCTTTACTTATTAC
*
1262 TCTTTACTTTTTAC
1 TCTTTACTTATTAC
1276 T
1 T
1277 AATTACCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 1 0.03
14 36 0.97
ACGTcount: A:0.18, C:0.21, G:0.02, T:0.60
Consensus pattern (14 bp):
TCTTTACTTATTAC
Found at i:1364 original size:64 final size:64
Alignment explanation
Indices: 1264--1507 Score: 202
Period size: 64 Copynumber: 3.9 Consensus size: 64
1254 CTTATTACTC
* ** *
1264 TTTACTTTTTACTAATTACCATTTTACTTTAAACTGATTACCCTTTTACAATTTT-CTAATTACC
1 TTTACTTTTTACTGATTA-C-TTTTACTTTTTACTGATTACCATTTTAC-ATTTTACTAATTACC
1328 AT
63 AT
* * * *
1330 TTTACTTTTCACTGATTACTTTTACTTTTTACTGATTACCATTTTACTTTTTATTAATTACCTT
1 TTTACTTTTTACTGATTACTTTTACTTTTTACTGATTACCATTTTACATTTTACTAATTACCAT
* ** * *
1394 TTTACTTTTTACTGATTGCCATTACTTCTTACTGA-T--CATTATTAC-TCTTTACTGATTACCA
1 TTTACTTTTTACTGATTACTTTTACTTTTTACTGATTACCATT-TTACAT-TTTACTAATTACCA
1455 T
64 T
* ** *
1456 ATTT--TCTTTACTGATTACTTTTTAC--TTTACTCTTTACCATTTT-CTTTTTACT
1 -TTTACTTTTTACTGATTAC-TTTTACTTTTTACTGATTACCATTTTACATTTTACT
1508 GATCTCTCTT
Statistics
Matches: 146, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
60 5 0.03
61 25 0.17
62 23 0.16
63 12 0.08
64 64 0.44
65 1 0.01
66 16 0.11
ACGTcount: A:0.23, C:0.19, G:0.03, T:0.55
Consensus pattern (64 bp):
TTTACTTTTTACTGATTACTTTTACTTTTTACTGATTACCATTTTACATTTTACTAATTACCAT
Found at i:1473 original size:35 final size:34
Alignment explanation
Indices: 1434--1725 Score: 184
Period size: 35 Copynumber: 8.1 Consensus size: 34
1424 ACTGATCATT
**
1434 ATTACTCTTTACTGATTACCATATTTTCTTTACTG
1 ATTACTCTTTACTCTTTACCAT-TTTTCTTTACTG
*
1469 ATTACTTTTTACTTTACTCTTTACCATTTTCTTTTTACTG
1 ATTAC----T-CTTTACTCTTTACCATTTT-TCTTTACTG
* *
1509 ATCT-CTCTTTA--CTTTACTC-TTTACTCTACCATTTTGCTA
1 AT-TACTCTTTACTCTTTAC-CATTT--T-T--C--TTTACTG
* *
1548 ATTACTCTTCATTCTTTACCATTTTTCCTTTACTG
1 ATTACTCTTTACTCTTTACCATTTTT-CTTTACTG
*
1583 ATTACTCTTTACTCTTTACCATTTTT-TTTCACTA
1 ATTACTCTTTACTCTTTACCATTTTTCTTT-ACTG
*
1617 ATTACTCTATTACTAC-TTACCATTTCTCTTTACTG
1 ATTACTCT-TTACT-CTTTACCATTTTTCTTTACTG
* ** *
1652 ATTACTTTTTACTCTTTATTATTTTACTGTTTACTG
1 ATTACTCTTTACTCTTTACCATTTT--TCTTTACTG
* *
1688 ATTAC-CATTACTTTTTACCATTTTACTCTTTACTG
1 ATTACTCTTTACTCTTTACCATTTT--TCTTTACTG
1723 ATT
1 ATT
1726 GCCTTTTCAA
Statistics
Matches: 207, Mismatches: 25, Indels: 50
0.73 0.09 0.18
Matches are distributed among these distances:
33 13 0.06
34 24 0.12
35 94 0.45
36 18 0.09
37 2 0.01
38 2 0.01
39 18 0.09
40 26 0.13
41 10 0.05
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.54
Consensus pattern (34 bp):
ATTACTCTTTACTCTTTACCATTTTTCTTTACTG
Found at i:1676 original size:69 final size:68
Alignment explanation
Indices: 1563--1725 Score: 186
Period size: 69 Copynumber: 2.3 Consensus size: 68
1553 TCTTCATTCT
*
1563 TTACCATTTTTCCTTTACTGATTACTCTTTACTCTTTACCATTTT-T-TTTCACTAATTACTCTA
1 TTACCATTTCT-CTTTACTGATTACTCTTTACTCTTTACCATTTTATGTTT-ACTAATTAC-C-A
1626 TTACTAC
62 TTACTAC
* ** *
1633 TTACCATTTCTCTTTACTGATTACTTTTTACTCTTTATTATTTTACTGTTTACTGATTACCATTA
1 TTACCATTTCTCTTTACTGATTACTCTTTACTCTTTACCATTTTA-TGTTTACTAATTACCATTA
**
1698 CTTT
65 CTAC
1702 TTACCATTTTACTCTTTACTGATT
1 TTACCA-TTT-CTCTTTACTGATT
1726 GCCTTTTCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
69 42 0.52
70 14 0.17
71 22 0.27
72 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (68 bp):
TTACCATTTCTCTTTACTGATTACTCTTTACTCTTTACCATTTTATGTTTACTAATTACCATTAC
TAC
Found at i:1856 original size:53 final size:53
Alignment explanation
Indices: 1799--1929 Score: 217
Period size: 53 Copynumber: 2.5 Consensus size: 53
1789 TACTATCGCG
*
1799 CTTTTCTTACTCTTTTTACTGAATATTATTTCCTACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATCATTTCCTACTCTTTTTACTGATGACT
* * * *
1852 CTTTTCTTATTCTTTTTACTGAATATCGTTTCTTACTCTTTTTACTGATGGCT
1 CTTTTCTTACTCTTTTTACTGAATATCATTTCCTACTCTTTTTACTGATGACT
1905 CTTTTCTTACTCTTTTTACTGAATA
1 CTTTTCTTACTCTTTTTACTGAATA
1930 CTGATTACTA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 72 1.00
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.56
Consensus pattern (53 bp):
CTTTTCTTACTCTTTTTACTGAATATCATTTCCTACTCTTTTTACTGATGACT
Found at i:1857 original size:27 final size:25
Alignment explanation
Indices: 1799--1926 Score: 150
Period size: 27 Copynumber: 4.9 Consensus size: 25
1789 TACTATCGCG
1799 CTTTTCTTACTCTTTTTACTGAATAT
1 CTTTTCTTACTCTTTTTACTG-ATAT
*
1825 -TATTTCCTACTCTTTTTACTGATGACT
1 CT-TTTCTTACTCTTTTTACTGAT-A-T
*
1852 CTTTTCTTATTCTTTTTACTGAATAT
1 CTTTTCTTACTCTTTTTACTG-ATAT
* *
1878 CGTTTCTTACTCTTTTTACTGATGGCT
1 CTTTTCTTACTCTTTTTACTGAT--AT
1905 CTTTTCTTACTCTTTTTACTGA
1 CTTTTCTTACTCTTTTTACTGA
1927 ATACTGATTA
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
25 5 0.06
26 39 0.44
27 41 0.47
28 3 0.03
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.56
Consensus pattern (25 bp):
CTTTTCTTACTCTTTTTACTGATAT
Found at i:6499 original size:17 final size:17
Alignment explanation
Indices: 6479--6512 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6469 TAAGTTACAG
6479 ATTTTTCAAAAAATAAT
1 ATTTTTCAAAAAATAAT
6496 ATTTTTCAAAAAATAAT
1 ATTTTTCAAAAAATAAT
6513 CGACGGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTTTCAAAAAATAAT
Found at i:7095 original size:166 final size:163
Alignment explanation
Indices: 6674--7112 Score: 578
Period size: 165 Copynumber: 2.6 Consensus size: 163
6664 TGAGTCATTT
*
6674 GTCAATTGAGAAATGACAAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAAT-CCCTCAAGAATCAAAAGTTAGG-CAT
* * * * ** *
6739 TTAAGTAATCTGCCAAGTAGGTAAAGAGGAAAAAGATTAGTT-TTCTAACTCATCATCAATCCTT
63 TTAAGTAATCTGTCAAGTAGGAAAAGA-CAAAAAAATTAGTTCTTCTAACTCAAAAGCAATCCTT
* * *
6803 GATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
127 GATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
6840 GTCCATTGAGAAATGACCAAAAAATTACTTATTTAATCCTCTCAAGAATCAAAAGTTAGTACATT
1 GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCC-CTCAAGAATCAAAAGTTAG-GCATT
*
6905 TAAGTAATCTGTCAAGTAGGAAAAGACAAAAAAAATAGTTCTT-TAACTCCAAAAGCAAGT-CTT
64 TAAGTAATCTGTCAAGTAGGAAAAGACAAAAAAATTAGTTCTTCTAACT-CAAAAGCAA-TCCTT
*
6968 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
127 GATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
7005 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAAGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATC-CCTCAAGAATCAAAAGTT-AGGCAT
* * *
7070 TTAAGTAATCGGTCAAGTGGGAAAAGACGAAAAAATTAGTTCT
63 TTAAGTAATCTGTCAAGTAGGAAAAGACAAAAAAATTAGTTCT
7113 CTCGCTCCTC
Statistics
Matches: 240, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
164 18 0.08
165 126 0.52
166 93 0.39
167 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (163 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCTCAAGAATCAAAAGTTAGGCATTTA
AGTAATCTGTCAAGTAGGAAAAGACAAAAAAATTAGTTCTTCTAACTCAAAAGCAATCCTTGATA
GGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:11837 original size:21 final size:20
Alignment explanation
Indices: 11801--11842 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
11791 TTCTCACAAT
*
11801 TTATTTCTGTAGTCATTTAA
1 TTATTTCTGTAGTCATGTAA
11821 TTATTATCTGT-GATCATGTAA
1 TTATT-TCTGTAG-TCATGTAA
11842 T
1 T
11843 CTTCATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
TTATTTCTGTAGTCATGTAA
Found at i:16762 original size:2 final size:2
Alignment explanation
Indices: 16751--16789 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
16741 ATTGTCGTAA
*
16751 AT AT -T AT AT AT AA 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
16790 TCTGAAGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17742 original size:53 final size:53
Alignment explanation
Indices: 17660--17762 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
17650 TCTATAAGAA
17660 AAGGTTTGGTAACCTTAAATTTGACCACAATTTGTCAAGACATAATCAAATTT
1 AAGGTTTGGTAACCTTAAATTTGACCACAATTTGTCAAGACATAATCAAATTT
* * *
17713 AAGGTTTGGTAACCTTAAATTTTAGCACAATTTGTCAGGACATAATCAAA
1 AAGGTTTGGTAACCTTAAATTTGACCACAATTTGTCAAGACATAATCAAA
17763 AGAAATGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (53 bp):
AAGGTTTGGTAACCTTAAATTTGACCACAATTTGTCAAGACATAATCAAATTT
Found at i:22063 original size:53 final size:54
Alignment explanation
Indices: 21654--22548 Score: 1177
Period size: 55 Copynumber: 16.4 Consensus size: 54
21644 AGGAGTAATC
21654 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC-AG
* *
21709 AGTAATTAAGTTAAAAATTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
* *
21763 AATAATTAAGCTAAAAAGTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCAAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC-AG
*
21818 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCAAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC-AG
* * * *
21873 TGTAATTAGGCTAAAAAGTAAAAGAAAGAGTAAACAGTAATTAGCTTAATTCAAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC-AG
21928 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC-AG
*
21983 AGTAATTAAGTTAAAAAGTAAAAGAAAGAGTAATCAGT-ATTAGTTTAATTCAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
* * * *
22036 AGTAATTAAGCTAAAAGGTAAAGGAAAGAGTAACCGGTAATTAGTTTAATTCAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
* *
22090 AGTAATTAAGCTAAAAAGTAAAA-AAA-AATAAACAGTAATTAGTTTAATTCAAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC-AG
22143 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
* * *
22197 AGTAATTAAGTTAAAAAGTAAAAGAGAGAGTAATCGGTAATTAGTTTAATATTAATATTCAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAG-----T-TT-A-ATTCAG
* *
22259 AGTAATTAAGCTAAAAAGT-AAAGAAAGTGTAATCAGTAATTAGTTTAATTCTG
1 AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
* * * *
22312 AGTAATTAAGATAAAAAAATAAAAGAAAGAGTAATCAATAA-AAGTTTAATTCAG
1 AGTAATTAAGCT-AAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
* * * *
22366 AATAATTAAGCTAAAAGGT-AAAGAAATG-GCAATCAGTGATTAGTTTAATTCAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAA-GAGTAATCAGTAATTAGTTTAATTCAG
* * *
22419 AGTAATTAAGCTAAAAAGT-AAAGAAATG-GTAATCAGTAAATGGTTTAATTTAG
1 AGTAATTAAGCTAAAAAGTAAAAGAAA-GAGTAATCAGTAATTAGTTTAATTCAG
* * * *
22472 AGTAATTAAACTAAAAAG-AGTAAA-AATG-GTAATCAGTAATT-GACTTGATTCAG
1 AGTAATTAAGCTAAAAAGTA--AAAGAAAGAGTAATCAGTAATTAG-TTTAATTCAG
* *
22525 AGTGATTAAGTTAAAAAGTAAAAG
1 AGTAATTAAGCTAAAAAGTAAAAG
22549 CAGTAATAAG
Statistics
Matches: 752, Mismatches: 65, Indels: 48
0.87 0.08 0.06
Matches are distributed among these distances:
52 40 0.05
53 195 0.26
54 176 0.23
55 291 0.39
56 1 0.00
59 1 0.00
60 2 0.00
61 22 0.03
62 24 0.03
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (54 bp):
AGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTCAG
Found at i:27982 original size:14 final size:14
Alignment explanation
Indices: 27963--27995 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
27953 TTTTAGTCAG
27963 TTAACCCTTAACAA
1 TTAACCCTTAACAA
27977 TTAACCCTTAACAA
1 TTAACCCTTAACAA
*
27991 ATAAC
1 TTAAC
27996 AAAGATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
TTAACCCTTAACAA
Found at i:28399 original size:15 final size:14
Alignment explanation
Indices: 28361--28400 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
28351 ACTCTCCATA
28361 GGAGAATGATTCTTG
1 GGAG-ATGATTCTTG
28376 GGAGA-GATTCTTG
1 GGAGATGATTCTTG
28389 GGAGAGTGATTC
1 GGAGA-TGATTC
28401 CAGTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.57
14 1 0.04
15 9 0.39
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (14 bp):
GGAGATGATTCTTG
Found at i:30322 original size:3 final size:3
Alignment explanation
Indices: 30314--30338 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30304 TGTAAACATT
30314 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
30339 ATAGCTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:32104 original size:9 final size:9
Alignment explanation
Indices: 32065--32107 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
32055 GGTCTCAAAT
32065 GAAAGAAAA
1 GAAAGAAAA
32074 GAAA-AAAA
1 GAAAGAAAA
32082 -AAAGAAAAA
1 GAAAG-AAAA
32091 GAAAGAAAA
1 GAAAGAAAA
32100 GAAAGAAA
1 GAAAGAAA
32108 GAACCTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 3 0.10
8 4 0.13
9 20 0.65
10 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:32503 original size:3 final size:3
Alignment explanation
Indices: 32466--32491 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
32456 GGGGGGAAAA
32466 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
32492 AATTGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46536 original size:30 final size:30
Alignment explanation
Indices: 46453--46601 Score: 208
Period size: 30 Copynumber: 4.9 Consensus size: 30
46443 GACATGGCAT
* * * * *
46453 GCCACGTGTACCAAAAAGTGACATGTGGCAC
1 GCCACGTGTA-TAAAAAATGACACGTGTCCC
* * *
46484 GTCACGTGTACCAAAAAGTGACACGTGTCCC
1 GCCACGTGTA-TAAAAAATGACACGTGTCCC
46515 GCCACGTGTATAAAAAATGACACGTGTCCC
1 GCCACGTGTATAAAAAATGACACGTGTCCC
46545 GCCACGTGTATAAAAAATGACACGTGTCCC
1 GCCACGTGTATAAAAAATGACACGTGTCCC
46575 GCCACGTGTATAAAAAATGACACGTGT
1 GCCACGTGTATAAAAAATGACACGTGT
46602 ACCAAAAGTG
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 75 0.68
31 36 0.32
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (30 bp):
GCCACGTGTATAAAAAATGACACGTGTCCC
Found at i:46608 original size:18 final size:18
Alignment explanation
Indices: 46577--46619 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
46567 CGTGTCCCGC
*
46577 CACGTGTATAAAAAATGA
1 CACGTGTACAAAAAATGA
* *
46595 CACGTGTACCAAAAGTGA
1 CACGTGTACAAAAAATGA
*
46613 CATGTGT
1 CACGTGT
46620 CATTTTTGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (18 bp):
CACGTGTACAAAAAATGA
Found at i:47028 original size:2 final size:2
Alignment explanation
Indices: 47021--47058 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
47011 GCTACGGTTC
* *
47021 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47059 CCATAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:49270 original size:12 final size:13
Alignment explanation
Indices: 49250--49290 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
49240 CCATTTTTCT
49250 TTTCTTTTTAGAC
1 TTTCTTTTTAGAC
49263 TTTCTTTTTAGGA-
1 TTTCTTTTTA-GAC
*
49276 -TTCCTTTTAGAC
1 TTTCTTTTTAGAC
49288 TTT
1 TTT
49291 GATGAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 12 0.50
14 2 0.08
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (13 bp):
TTTCTTTTTAGAC
Found at i:53736 original size:433 final size:430
Alignment explanation
Indices: 52981--53812 Score: 1134
Period size: 433 Copynumber: 1.9 Consensus size: 430
52971 AGACATAATG
** * * *
52981 GTAAAGGACTAAGTAGTATAAAATAGAAAAGTATGAGGCTCATTTGATAAATAATCCAATTAAAA
1 GTAAAGGACTAAAAAGTACAAAATAGAAAAATATGAGGCTCATTTGATAAATAATCCAAATAAAA
* * * * * *
53046 AATGTTTGTTGATTGGGGTCTTGAAACAAAAAAAAAAAATCCTTTTGACCCCTTAATGAAACTTG
66 AATGTTTGATGATAGAGATCTTG--A-AAAAAAAAAAAATCCTTTTGAACCCTTAATGAAACTCG
* * *
53111 TAGATCAAATTTAGCTTTCGGGTCCTTTATGAAATTCGTAGATCAGGCAATAATTAACCGGCACT
128 TAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAGATCAGGCAATAATTAACCGACACT
* * * * *
53176 TAAATAACTTTAATCGGACATGTGGATCCAAAATTATATGTTATTAGATAGACCGGCAATCGAAA
193 TAAATAACATTAATCGGACATGTGGATCCAAAATTATATGATATTAAAAAGACCGGCAATCAAAA
*
53241 CAACAAATTTGGGAAGCATTTTTTTTAAATTGAAAAATAAAAATTGGCTTTAGAGTCCTTCATGA
258 CAACAAATTTCGGAAGCATTTTTTTTAAATTGAAAAATAAAAATTGGCTTTAGAGTCCTTCATGA
* * *
53306 AAGTTTGT-GATCATGAAAATACCTTTTA-ATA-ACCTGAATCACCTTAATCGAACAAATAGAAA
323 AAG-TTGTAAATCATGAAAATACCTTTTATAGACACCTAAATCACCTTAATCGAACAAATAGAAA
53368 AAAAAAATAAAAGCTTAAGCATTAAATCGATTAGGATAGAATTA
387 AAAAAAATAAAAGCTTAAGCATTAAATCGATTAGGATAGAATTA
* *
53412 GTAAAGGACTAAAAAGTACAAAGTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAAC
1 GTAAAGGACTAAAAAGTACAAAATAGAAAAATATGAGGCTCATTTGATAAATAATCCAAATAAA-
* * *
53477 AAATGTTTGATGATAGAGATCTTG-AAATATAAAAATTCCTTTTTGAACCCTTAATGAAACTCGT
65 AAATGTTTGATGATAGAGATCTTGAAAAAAAAAAAAATCC-TTTTGAACCCTTAATGAAACTCGT
* *
53541 AGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAGATCATGCAATAACCTTTTAACTGAC
129 AGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAGATCAGGCAATAA----TTAACCGAC
* * *
53606 ACTTGAATAACATTAATCGGACATGTGGATCGAAAATTATATGATATTAAAAAGATCGGCAATCA
190 ACTTAAATAACATTAATCGGACATGTGGATCCAAAATTATATGATATTAAAAAGACCGGCAATCA
* * * * * *
53671 AAATCACCAAATTTCGTAAGCA-TTTTTTTGAATTGAAACATAAAATTTGGCTTTTGAGTCCTTC
255 AAA-CAACAAATTTCGGAAGCATTTTTTTTAAATTGAAAAATAAAAATTGGCTTTAGAGTCCTTC
* *
53735 ATGAAAGTTGTAAATCATGAAATTACCTTTTATTAGACACCTAAATCACCTTAATCGGACAAATA
319 ATGAAAGTTGTAAATCATGAAAATACCTTTTA-TAGACACCTAAATCACCTTAATCGAACAAATA
* *
53800 GGAATAAAAAATA
383 GAAAAAAAAAATA
53813 CCTAAAGCGT
Statistics
Matches: 347, Mismatches: 43, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
428 12 0.03
429 71 0.20
431 57 0.16
432 24 0.07
433 130 0.37
434 15 0.04
435 2 0.01
436 36 0.10
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (430 bp):
GTAAAGGACTAAAAAGTACAAAATAGAAAAATATGAGGCTCATTTGATAAATAATCCAAATAAAA
AATGTTTGATGATAGAGATCTTGAAAAAAAAAAAAATCCTTTTGAACCCTTAATGAAACTCGTAG
ATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAGATCAGGCAATAATTAACCGACACTTAA
ATAACATTAATCGGACATGTGGATCCAAAATTATATGATATTAAAAAGACCGGCAATCAAAACAA
CAAATTTCGGAAGCATTTTTTTTAAATTGAAAAATAAAAATTGGCTTTAGAGTCCTTCATGAAAG
TTGTAAATCATGAAAATACCTTTTATAGACACCTAAATCACCTTAATCGAACAAATAGAAAAAAA
AAATAAAAGCTTAAGCATTAAATCGATTAGGATAGAATTA
Found at i:57666 original size:25 final size:25
Alignment explanation
Indices: 57632--57687 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
57622 AATTAGGTGC
57632 TTTACACCTTTTGTACAGACTGGAG
1 TTTACACCTTTTGTACAGACTGGAG
57657 TTTACACCTTTTGTACAGACTGGAG
1 TTTACACCTTTTGTACAGACTGGAG
57682 -TTACAC
1 TTTACAC
57688 TCCAGTTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (25 bp):
TTTACACCTTTTGTACAGACTGGAG
Found at i:58937 original size:32 final size:30
Alignment explanation
Indices: 58876--58938 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
58866 CACATCACCT
*
58876 ACACTAAGAGAGGCCCAATACACTTCACAC
1 ACACTAAAAGAGGCCCAATACACTTCACAC
* *
58906 ACACTAAAAGAGGCCCAATGCACTTTACAC
1 ACACTAAAAGAGGCCCAATACACTTCACAC
58936 ACA
1 ACA
58939 TTAGAGGCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.32, G:0.13, T:0.14
Consensus pattern (30 bp):
ACACTAAAAGAGGCCCAATACACTTCACAC
Found at i:63104 original size:33 final size:32
Alignment explanation
Indices: 63054--63177 Score: 135
Period size: 33 Copynumber: 3.7 Consensus size: 32
63044 CCGCGCAACA
63054 CCGGCCACAAGACCGGCCACGCGACATGGACATG
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATG
63088 TCCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 -CCGGCCA-CAACCGGCCACGCGACATGGACAT-G
* ** *
63122 CCGGCTACAACCGGCCAAACGAC-TCGGCCATG
1 CCGGCCACAACCGGCCACGCGACAT-GGACATG
63154 CCTGGCCACAACCGGCCACGCGAC
1 CC-GGCCACAACCGGCCACGCGAC
63178 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
32 5 0.06
33 63 0.82
34 1 0.01
35 7 0.09
36 1 0.01
ACGTcount: A:0.23, C:0.41, G:0.27, T:0.08
Consensus pattern (32 bp):
CCGGCCACAACCGGCCACGCGACATGGACATG
Found at i:69349 original size:14 final size:14
Alignment explanation
Indices: 69330--69359 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
69320 ATCATATCAA
69330 TAAATAAAATCTCT
1 TAAATAAAATCTCT
69344 TAAATAAAATCTCT
1 TAAATAAAATCTCT
69358 TA
1 TA
69360 GTGAAGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAATAAAATCTCT
Found at i:72300 original size:37 final size:37
Alignment explanation
Indices: 72219--72402 Score: 224
Period size: 37 Copynumber: 5.2 Consensus size: 37
72209 CATGTGCATC
72219 AGTAAAAGCAGTTAAAGAACTTAATTCAGGG-AATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGCAATTA
* *
72255 AGTAAAAGCAGTTAAAGAACTTAATTTAGGACAATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGCAATTA
* *
72292 AGTAAAAGCAGTTAAGGAACTTAATTCTGGGCAATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGCAATTA
*
72329 AGT------AGTTAAAGAACTCAATTCAGGGCAATTA
1 AGTAAAAGCAGTTAAAGAACTTAATTCAGGGCAATTA
* * *
72360 AGTAAAAAGCAGCTAAA-ATCTTAATTCAGGGTAATTA
1 AGT-AAAAGCAGTTAAAGAACTTAATTCAGGGCAATTA
72397 AG-AAAA
1 AGTAAAA
72403 TAAAGTACAG
Statistics
Matches: 127, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
31 28 0.22
35 4 0.03
36 29 0.23
37 60 0.47
38 6 0.05
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (37 bp):
AGTAAAAGCAGTTAAAGAACTTAATTCAGGGCAATTA
Found at i:72336 original size:31 final size:31
Alignment explanation
Indices: 72301--72363 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
72291 AAGTAAAAGC
* * *
72301 AGTTAAGGAACTTAATTCTGGGCAATTAAGT
1 AGTTAAAGAACTCAATTCAGGGCAATTAAGT
72332 AGTTAAAGAACTCAATTCAGGGCAATTAAGT
1 AGTTAAAGAACTCAATTCAGGGCAATTAAGT
72363 A
1 A
72364 AAAAGCAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.29
Consensus pattern (31 bp):
AGTTAAAGAACTCAATTCAGGGCAATTAAGT
Found at i:72383 original size:68 final size:67
Alignment explanation
Indices: 72219--72398 Score: 193
Period size: 68 Copynumber: 2.6 Consensus size: 67
72209 CATGTGCATC
* * *
72219 AGTAAAAGCAGTTAAAGAACTTAATTCAGGG-AATTAAGTAAAAGCAGTTAAAGAACTTAATTTA
1 AGTAAAAGCAGCT-AAGAACTTAATTCAGGGCAATTAAGT------AGTTAAAGAACTCAATTCA
72283 GGACAATTA
59 GGACAATTA
* * *
72292 AGTAAAAGCAGTTAAGGAACTTAATTCTGGGCAATTAAGTAGTTAAAGAACTCAATTCAGGGCAA
1 AGTAAAAGCAGCTAA-GAACTTAATTCAGGGCAATTAAGTAGTTAAAGAACTCAATTCAGGACAA
72357 TTA
65 TTA
*
72360 AGTAAAAAGCAGCTAA-AATCTTAATTCAGGGTAATTAAG
1 AGT-AAAAGCAGCTAAGAA-CTTAATTCAGGGCAATTAAG
72399 AAAATAAAGT
Statistics
Matches: 96, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
67 2 0.02
68 46 0.48
69 11 0.11
72 2 0.02
73 27 0.28
74 8 0.08
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (67 bp):
AGTAAAAGCAGCTAAGAACTTAATTCAGGGCAATTAAGTAGTTAAAGAACTCAATTCAGGACAAT
TA
Found at i:72464 original size:71 final size:71
Alignment explanation
Indices: 72373--72562 Score: 317
Period size: 71 Copynumber: 2.7 Consensus size: 71
72363 AAAAAGCAGC
* *
72373 TAAAATCTTAATTCAGGGTAATTAAGAAAATAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
72438 GAAGAA
66 GAAGAA
* *
72444 TAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGAACAGTCAAGGTCCTAAGTTGGGCAATTAA
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
*
72509 GAGGAA
66 GAAGAA
* *
72515 TAAAGCCTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTC
1 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTC
72563 ATAGTTTGGA
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 110 1.00
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (71 bp):
TAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGCAATTAA
GAAGAA
Found at i:72913 original size:41 final size:40
Alignment explanation
Indices: 72588--72916 Score: 408
Period size: 41 Copynumber: 8.1 Consensus size: 40
72578 AAGATGAGTA
* * *
72588 AAGTTCTAATCCAAGGCGATTAAGAAAGTCAAACATAGATA
1 AAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAG-TT
* *
72629 AAGTTTTAATCCAGGGCGATTAAGAAAGTCAAAGATAGTC
1 AAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
* *
72669 AAGGTTTTAATCCAGGGCGATTAAGAAAGTCCAATATAGTT
1 AA-GTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
* * *
72710 AAGGTTTTAATCCAGGGCGATTAAGAAAGTCGAAGATAGTC
1 AA-GTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
*
72751 AAGGTTTTAATCCAGGGCGATTAAGAAAGTCCAACATAGTT
1 AA-GTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
72792 AAAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
1 -AAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
* ** * **
72833 AAAG-TTTATTCTGGGGTGATTAAGAAAGTCAGGCATAGTT
1 -AAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
* **
72873 AAGTTTTTAATCCAGGGTGATTAAGAAAGGGAAACATAGTT
1 AAG-TTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
72914 AAG
1 AAG
72917 AACTTAATTC
Statistics
Matches: 257, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
39 3 0.01
40 33 0.13
41 219 0.85
42 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (40 bp):
AAGTTTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTT
Found at i:72958 original size:37 final size:36
Alignment explanation
Indices: 72910--73209 Score: 366
Period size: 37 Copynumber: 8.2 Consensus size: 36
72900 AGGGAAACAT
* *
72910 AGTTAAGAACTTAATTCAGAGCAATTAAGTAAGAGC
1 AGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
*
72946 AGGTTAAGAACTTAATTCAGGGGAATTAAGTAAAAGC
1 A-GTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
* * *
72983 AGGTAAACAACTTAATTCAAGGGTAATTAAGTAAAAGC
1 A-GTTAAGAACTTAATTC-AGGGCAATTAAGTAAAAGC
* * *
73021 AGGTTAAGAGCTTAATTTAGGACAATTAAGTAAAAGC
1 A-GTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
* **
73058 AGTAAAGAACTTAATTCAGGATAATTAAGTAAAAAGC
1 AGTTAAGAACTTAATTCAGGGCAATTAAGT-AAAAGC
* *
73095 AGTTAAGAACTTAGTTCAGGACAATTAAGTAAAAGC
1 AGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
* * *
73131 AATTAAGAACTTAATTTAGGGAAATTAAGTAAAAGC
1 AGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
* * *
73167 AGTTGAAGGACTTAATTCAGGGTAATTAAGTAAAAAC
1 AGTT-AAGAACTTAATTCAGGGCAATTAAGTAAAAGC
73204 AGTTAA
1 AGTTAA
73210 AAGGTAAGGA
Statistics
Matches: 231, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
36 68 0.29
37 131 0.57
38 32 0.14
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (36 bp):
AGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
Found at i:73116 original size:73 final size:73
Alignment explanation
Indices: 72914--73206 Score: 360
Period size: 73 Copynumber: 4.0 Consensus size: 73
72904 AAACATAGTT
* * **
72914 AAGAACTTAATTCA-GAGCAATTAAGTAAGAGCAGGTTAAGAACTTAATTCAGGGGAATTAAGTA
1 AAGAACTTAATTCAGGA-TAATTAAGTAAAAGCAGGTTAAGAACTTAATTCAGGACAATTAAGTA
72978 AAAGCAGGTA
65 AAAGCA-GTA
* * * *
72988 AACAACTTAATTCAAGGGTAATTAAGTAAAAGCAGGTTAAGAGCTTAATTTAGGACAATTAAGTA
1 AAGAACTTAATTC-AGGATAATTAAGTAAAAGCAGGTTAAGAACTTAATTCAGGACAATTAAGTA
73053 AAAGCAGTA
65 AAAGCAGTA
*
73062 AAGAACTTAATTCAGGATAATTAAGTAAAAAGCA-GTTAAGAACTTAGTTCAGGACAATTAAGTA
1 AAGAACTTAATTCAGGATAATTAAGT-AAAAGCAGGTTAAGAACTTAATTCAGGACAATTAAGTA
* *
73126 AAAGCAATT
65 AAAGCAGTA
* * **
73135 AAGAACTTAATTTAGGGA-AATTAAGTAAAAGCA-GTTGAAGGACTTAATTCAGGGTAATTAAGT
1 AAGAACTTAATTCA-GGATAATTAAGTAAAAGCAGGTT-AAGAACTTAATTCAGGACAATTAAGT
*
73198 AAAAACAGT
64 AAAAGCAGT
73207 TAAAAGGTAA
Statistics
Matches: 192, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
72 10 0.05
73 96 0.50
74 37 0.19
75 48 0.25
76 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (73 bp):
AAGAACTTAATTCAGGATAATTAAGTAAAAGCAGGTTAAGAACTTAATTCAGGACAATTAAGTAA
AAGCAGTA
Found at i:73274 original size:41 final size:40
Alignment explanation
Indices: 73229--73474 Score: 244
Period size: 41 Copynumber: 6.3 Consensus size: 40
73219 ATAGGCACAT
73229 ACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCATAG
1 ACTTAATTTC-AGGAAGGAAATTAGGTAAAAACAAGCATAG
* * **
73270 ACTTAA-TTCA-G--GGTAATTAAGT-AAAGTAAGCATAG
1 ACTTAATTTCAGGAAGGAAATTAGGTAAAAACAAGCATAG
*
73305 ACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAG
1 ACTTAATTTC-AGGAAGGAAATTAGGTAAAAACAAGCATAG
* * ** *
73346 ACTTAA-TTCA-G--GGTAATTAAGT-AAAGTAAGCACAG
1 ACTTAATTTCAGGAAGGAAATTAGGTAAAAACAAGCATAG
* *
73381 ACTTAATTTCAGTGAAGGAAATTAGGTAAAGATAAGCATAG
1 ACTTAATTTCAG-GAAGGAAATTAGGTAAAAACAAGCATAG
* * *
73422 ACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAT
1 ACTTAATTTC-AGGAAGGAAATTAGGTAAAAACAAGCATAG
73463 ACTTAA-TTCAGG
1 ACTTAATTTCAGG
73475 GTAATTAAGT
Statistics
Matches: 169, Mismatches: 23, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
35 32 0.19
36 25 0.15
37 1 0.01
38 4 0.02
39 5 0.03
40 27 0.16
41 73 0.43
42 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (40 bp):
ACTTAATTTCAGGAAGGAAATTAGGTAAAAACAAGCATAG
Found at i:73355 original size:76 final size:76
Alignment explanation
Indices: 73223--73429 Score: 362
Period size: 76 Copynumber: 2.7 Consensus size: 76
73213 GTAAGGATAG
* *
73223 GCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
73288 AAGTAAAGTAA
66 AAGTAAAGTAA
*
73299 GCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
73364 AAGTAAAGTAA
66 AAGTAAAGTAA
*
73375 GCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGATAAGCATAGACTTAATT
1 GCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAATT
73430 TCAAGGAAGG
Statistics
Matches: 125, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
75 2 0.02
76 123 0.98
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (76 bp):
GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
AAGTAAAGTAA
Found at i:73417 original size:117 final size:115
Alignment explanation
Indices: 73284--73522 Score: 380
Period size: 117 Copynumber: 2.1 Consensus size: 115
73274 AATTCAGGGT
*
73284 AATTAAGTAAAGTAAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACT
1 AATTAAGTAAAGTAAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
73349 TAATTCAGGGTAATTAAGTAAAGTAAGCACA-GACTTAATTTCAGTGAAGGA
66 TAATTCAGGGTAATTAAGTAAA-TAAGCA-ATGACTTAATTTCAGTGAAGGA
* *
73400 AATTAGGTAAAGATAAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACATAC
1 AATTAAGTAAAG-TAAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
*
73465 TTAATTCAGGGTAATTAAGTAAATTAGCAATGACTTAATTTCA-T-AA-G-
65 TTAATTCAGGGTAATTAAGTAAATAAGCAATGACTTAATTTCAGTGAAGGA
73512 AATTAAGTAAA
1 AATTAAGTAAA
73523 ATCATCAAAG
Statistics
Matches: 116, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
112 10 0.09
113 1 0.01
114 2 0.02
115 2 0.02
116 28 0.24
117 73 0.63
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (115 bp):
AATTAAGTAAAGTAAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
TAATTCAGGGTAATTAAGTAAATAAGCAATGACTTAATTTCAGTGAAGGA
Found at i:73746 original size:37 final size:37
Alignment explanation
Indices: 73585--73743 Score: 248
Period size: 37 Copynumber: 4.3 Consensus size: 37
73575 ACCTCCGGGG
* * *
73585 ATTAAGTAAAGAAAAGGACTTGGTTCCAAGGAAGGGA
1 ATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGA
*
73622 ATTAAGTAGAGCAATA-GACTTGATTCCAAAGAAGGGA
1 ATTAAGTAGAGCAA-AGGACTTGATTCCAAGGAAGGGA
73659 ATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGA
* *
73696 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGAGA
1 ATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGA
73733 ATTAAGTAGAG
1 ATTAAGTAGAG
73744 TAAGG
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
36 1 0.01
37 111 0.98
38 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.21
Consensus pattern (37 bp):
ATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGA
Done.