Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011829.1 Corchorus olitorius cultivar O-4 contig11862, 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: 41121
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:282 original size:25 final size:23
Alignment explanation
Indices: 239--286 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
229 TGATTGAGCT
*
239 TTGAAAGTTTGAAGGTTGAGAGAA
1 TTGAAAATTTGAAGGTTGA-AGAA
*
263 TTGAAAATATTGAAGTTTGAAGAA
1 TTGAAAAT-TTGAAGGTTGAAGAA
287 AATAAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (23 bp):
TTGAAAATTTGAAGGTTGAAGAA
Found at i:525 original size:22 final size:22
Alignment explanation
Indices: 483--526 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
473 TATTCATATG
*
483 AAATTATGATAATCTCCCTATT
1 AAATTATGATAATCTCACTATT
505 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
527 TTTGATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:551 original size:22 final size:22
Alignment explanation
Indices: 526--578 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
516 ATTACACTAT
*
526 TTTTGATTA-CCTCCTTATGAAA
1 TTTTGATAAGCCTCC-TATGAAA
*
548 TTTTGATAAGCTTCCTATGAAA
1 TTTTGATAAGCCTCCTATGAAA
*
570 TTTTAATAA
1 TTTTGATAA
579 CGATACTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (22 bp):
TTTTGATAAGCCTCCTATGAAA
Found at i:728 original size:45 final size:45
Alignment explanation
Indices: 671--789 Score: 118
Period size: 45 Copynumber: 2.7 Consensus size: 45
661 TGAAGATCTT
* * *
671 ACTATGAAATGTTGATAACTTCCCA-ATGAAATTTTGATAACCAAC
1 ACTATGAAATGTTAATAACCT-CCATATGAAATATTGATAACCAAC
* *
716 ACTATGAGATGTTAATAACCTCCATATGATATATTGATAACC-AC
1 ACTATGAAATGTTAATAACCTCCATATGAAATATTGATAACCAAC
** * *
760 GTTATGAAAAT-TTAAAAATCTCCATATGAA
1 ACTATG-AAATGTTAATAACCTCCATATGAA
790 TTGTTAGTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
44 25 0.41
45 36 0.59
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (45 bp):
ACTATGAAATGTTAATAACCTCCATATGAAATATTGATAACCAAC
Found at i:841 original size:22 final size:21
Alignment explanation
Indices: 810--1098 Score: 180
Period size: 22 Copynumber: 13.5 Consensus size: 21
800 TCACACTCTA
* *
810 AAATTGTGATAACATCGCTATG
1 AAATTTTGATAACCTC-CTATG
*
832 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGAT-AACC-TCCTATG
* *
855 AAATTTTCATAAACCTCCCTATA
1 AAATTTTGAT-AACCT-CCTATG
*
878 AAATTTTGATAATCTCCTTATG
1 AAATTTTGATAACCTCC-TATG
* *
900 AAATCTTGATAA----CTA-C
1 AAATTTTGATAACCTCCTATG
916 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATAACC-TCCTATG
** * *
938 ATTTTTTTATAACCTCATTATG
1 AAATTTTGATAACCTC-CTATG
* *
960 AAATTTTGTTAATCTCCTTATG
1 AAATTTTGATAACCTCC-TATG
* * *
982 AAATTTTGATCTACATACTATG
1 AAATTTTGAT-AACCTCCTATG
*
1004 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAA-CCTCCTATG
* **
1026 AAATTTTGA-AAACTAAATTATG
1 AAATTTTGATAACCT--CCTATG
*
1048 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACC-TCCTATG
* *
1070 AAATTTTGATATCCTCC-CTG
1 AAATTTTGATAACCTCCTATG
1090 -AATTTTGAT
1 AAATTTTGAT
1099 TACTCCATAA
Statistics
Matches: 211, Mismatches: 38, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
19 9 0.04
20 4 0.02
21 12 0.06
22 127 0.60
23 42 0.20
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATG
Found at i:858 original size:23 final size:23
Alignment explanation
Indices: 808--911 Score: 104
Period size: 23 Copynumber: 4.6 Consensus size: 23
798 AATCACACTC
* * *
808 TAAAATTGTGAT-AACATCGCTA
1 TAAAATTTTGATAAACCTCCCTA
* *
830 TGAAATTTTGATAAACCTTCCTA
1 TAAAATTTTGATAAACCTCCCTA
*
853 TAAAATTTTCATAAACCTCCCTA
1 TAAAATTTTGATAAACCTCCCTA
* *
876 TAAAATTTTGAT-AATCTCCTTA
1 TAAAATTTTGATAAACCTCCCTA
* *
898 TGAAATCTTGATAA
1 TAAAATTTTGATAA
912 CTACAAATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
22 28 0.42
23 39 0.58
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (23 bp):
TAAAATTTTGATAAACCTCCCTA
Found at i:973 original size:82 final size:84
Alignment explanation
Indices: 832--991 Score: 225
Period size: 82 Copynumber: 1.9 Consensus size: 84
822 CATCGCTATG
*
832 AAATTTTGATAAACCTTCCTATAAAATTTTCATAAACCTCCCTATAAAATTTTGATAATCTCCTT
1 AAATTTTGATAAACCTTCCTATAAAATTTTCATAAACCTCACTATAAAATTTTGATAATCTCCTT
897 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGATAACTAC
* ** * * * *
916 AAATTTTGAT-AACCTTCCTATGATTTTTTTAT-AACCTCATTATGAAATTTTGTTAATCTCCTT
1 AAATTTTGATAAACCTTCCTATAAAATTTTCATAAACCTCACTATAAAATTTTGATAATCTCCTT
*
979 ATGAAATTTTGAT
66 ATGAAATCTTGAT
992 CTACATACTA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
82 39 0.58
83 18 0.27
84 10 0.15
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.43
Consensus pattern (84 bp):
AAATTTTGATAAACCTTCCTATAAAATTTTCATAAACCTCACTATAAAATTTTGATAATCTCCTT
ATGAAATCTTGATAACTAC
Found at i:1238 original size:22 final size:21
Alignment explanation
Indices: 1206--1430 Score: 89
Period size: 22 Copynumber: 10.3 Consensus size: 21
1196 TCACATTTTG
* *
1206 AAAATTTGATAACTTCTTTAT
1 AAAATTTGATAACCTCTCTAT
1227 AAAATTTTGATAACCTCTCTAT
1 AAAA-TTTGATAACCTCTCTAT
* * *
1249 AAAAATTTGTTGACCCCTCTAT
1 -AAAATTTGATAACCTCTCTAT
* *
1271 GAAATTTTGATAAACACAT-TCTGT
1 -AAAATTTGAT-AAC-C-TCTCTAT
* * *
1295 -AATTTTGATAACCTCGCTTT
1 AAAATTTGATAACCTCTCTAT
* ** *
1315 GAAATTTTGATAACAACACTAT
1 -AAAATTTGATAACCTCTCTAT
* *
1337 GAAATTTTGATAATCT-TCCTAT
1 -AAAATTTGATAACCTCT-CTAT
*
1359 AAATTTTGATAATCCGGTCTCTAT
1 AAAATTTGATAA-CC--TCTCTAT
* * *
1383 GAAATTTCGATAATCACTCTAT
1 AAAATTT-GATAACCTCTCTAT
* * *
1405 GAGATTTGATAACAT-TCTAT
1 AAAATTTGATAACCTCTCTAT
*
1425 CAAATT
1 AAAATT
1431 CTGGTACTCC
Statistics
Matches: 158, Mismatches: 32, Indels: 29
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 13 0.08
21 24 0.15
22 92 0.58
23 6 0.04
24 16 0.10
25 6 0.04
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
AAAATTTGATAACCTCTCTAT
Found at i:1318 original size:44 final size:45
Alignment explanation
Indices: 1267--1370 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 45
1257 GTTGACCCCT
* * *
1267 CTATGAAATTTTGATAAAC-ACATTCTGTAATTTTGATAA-CCTC
1 CTATGAAATTTTGATAAACAACACTATGAAATTTTGATAATCCTC
* *
1310 GCTTTGAAATTTTGAT-AACAACACTATGAAATTTTGATAATCTTC
1 -CTATGAAATTTTGATAAACAACACTATGAAATTTTGATAATCCTC
1355 CTAT-AAATTTTGATAA
1 CTATGAAATTTTGATAA
1371 TCCGGTCTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
43 13 0.25
44 35 0.69
45 3 0.06
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (45 bp):
CTATGAAATTTTGATAAACAACACTATGAAATTTTGATAATCCTC
Found at i:1485 original size:22 final size:21
Alignment explanation
Indices: 1456--1595 Score: 65
Period size: 22 Copynumber: 6.4 Consensus size: 21
1446 AAATTGAGAC
*
1456 TTTT-ATAACCTTTATATGAAA
1 TTTTGATAACCTAT-TATGAAA
1477 TTTTGATAATCAC-ATTATGAAA
1 TTTTGATAA-C-CTATTATGAAA
**
1499 TTTTGATAACCTCCCTATGAAA
1 TTTTGATAACCT-ATTATGAAA
* * *
1521 -TATCAGTAACCTCCTTATGAAA
1 TTTTGA-TAACCT-ATTATGAAA
* *
1543 TTTTGTTAA-CTACACTATGAAA
1 TTTTGATAACCT--ATTATGAAA
* *
1565 TTCTT-ATAACCTCGTTATGACA
1 TT-TTGATAACCT-ATTATGAAA
1587 TTTTGATAA
1 TTTTGATAA
1596 TCTCTTTGAT
Statistics
Matches: 93, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.01
21 12 0.13
22 71 0.76
23 8 0.09
24 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (21 bp):
TTTTGATAACCTATTATGAAA
Found at i:1518 original size:44 final size:43
Alignment explanation
Indices: 1470--1595 Score: 128
Period size: 44 Copynumber: 2.9 Consensus size: 43
1460 ATAACCTTTA
* * *
1470 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCT-CCC
1 TATGAAATTTT-ATAACCTCATTATGAAATTTTGATAA-CTACAC
* * * *
1514 TATGAAATATCAGTAACCTCCTTATGAAATTTTGTTAACTACAC
1 TATGAAATTTTA-TAACCTCATTATGAAATTTTGATAACTACAC
* *
1558 TATGAAATTCTTATAACCTCGTTATGACATTTTGATAA
1 TATGAAATT-TTATAACCTCATTATGAAATTTTGATAA
1596 TCTCTTTGAT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.04
44 62 0.93
45 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTATAACCTCATTATGAAATTTTGATAACTACAC
Found at i:1708 original size:67 final size:66
Alignment explanation
Indices: 1600--1788 Score: 195
Period size: 67 Copynumber: 2.8 Consensus size: 66
1590 TGATAATCTC
* * * * * * *
1600 TTTGATAACCTTTC-TATCAAATTGTGATAACCACTATTATGAAATTTCAATAACCTTCCTAAAA
1 TTTGATAA-CTTCCATATGAAATTTTGGTAACCAC-ACTATGAAATTTTAATAACCTTCCCAAAA
1664 AAT
64 AAT
* * **
1667 TTTGATAACCTGGTCC-TGTGAAATTTTGGTAACCAC-CTATGAAATTTTGATAACCTTCCCATG
1 TTTGATAA-CT--TCCATATGAAATTTTGGTAACCACACTATGAAATTTTAATAACCTTCCCAAA
1730 AAAT
63 AAAT
* *
1734 TTTGATAACTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTTATAACCT
1 TTTGATAACTTCCATATGAAATTTTGGTAACCACACTATGAAATTTTAATAACCT
1789 CCTCATGAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
64 3 0.03
65 19 0.18
66 20 0.19
67 44 0.42
69 18 0.17
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (66 bp):
TTTGATAACTTCCATATGAAATTTTGGTAACCACACTATGAAATTTTAATAACCTTCCCAAAAAA
T
Found at i:1733 original size:22 final size:22
Alignment explanation
Indices: 1600--1831 Score: 184
Period size: 22 Copynumber: 10.5 Consensus size: 22
1590 TGATAATCTC
* *
1600 TTTGATAACCTTTCTATCAAAT
1 TTTGATAACCTTCCTATGAAAT
* * **
1622 TGTGATAACCACTATTATGAAAT
1 TTTGATAACC-TTCCTATGAAAT
** **
1645 TTCAATAACCTTCCTAAAAAAT
1 TTTGATAACCTTCCTATGAAAT
*
1667 TTTGATAACCTGGTCCTGTGAAAT
1 TTTGATAACCT--TCCTATGAAAT
* *
1691 TTTGGTAACC-ACCTATGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
1712 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
1734 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCTTCC-TATGAAAT
* * *
1756 TTTGGTAACC-ACACTATGGAAT
1 TTTGATAACCTTC-CTATGAAAT
*
1778 TTTTATAACC-TCCTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * * *
1800 TATAATAACCATCTTATGAAAT
1 TTTGATAACCTTCCTATGAAAT
1822 TTTGATAACC
1 TTTGATAACC
1832 ACACAAAGAC
Statistics
Matches: 164, Mismatches: 37, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
21 25 0.15
22 102 0.62
23 20 0.12
24 17 0.10
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:1796 original size:66 final size:66
Alignment explanation
Indices: 1600--1835 Score: 244
Period size: 66 Copynumber: 3.5 Consensus size: 66
1590 TGATAATCTC
* * * * * ** * **
1600 TTTGATAACCTTTCTATCAAATTGTGATAACCACTATTATGAAATTTCAATAACCTTCCTAAAAA
1 TTTGATAACCTTCCTATGAAATTTTGGTAACCAC-ACTATGAAATTTTGATAACCTTCCCATGAA
1665 AT
65 AT
*
1667 TTTGATAACCTGGTCCTGTGAAATTTTGGTAACCAC-CTATGAAATTTTGATAACCTTCCCATGA
1 TTTGATAACCT--TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGA
1731 AAT
64 AAT
* *
1734 TTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTTATAACC-TCCTCATGA
1 TTTGATAACCTTCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGA
1797 AAT
64 AAT
* * * * *
1800 TATAATAACCATCTTATGAAATTTTGATAACCACAC
1 TTTGATAACCTTCCTATGAAATTTTGGTAACCACAC
1836 AAAGACAAGA
Statistics
Matches: 144, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
64 3 0.02
65 22 0.15
66 54 0.38
67 47 0.33
69 18 0.12
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (66 bp):
TTTGATAACCTTCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAA
T
Found at i:2349 original size:30 final size:27
Alignment explanation
Indices: 2295--2349 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
2285 GTCTAAATTG
**
2295 AAATTTTATAATTAATTTCTAAATAAT
1 AAATTTTATAATTAATTTAGAAATAAT
2322 AAATTTTAATAATGTCAATTTAGAAATA
1 AAATTTT-ATAAT-T-AATTTAGAAATA
2350 TATTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 5 0.22
29 1 0.04
30 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
AAATTTTATAATTAATTTAGAAATAAT
Found at i:3525 original size:11 final size:11
Alignment explanation
Indices: 3509--3539 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3499 CTTGTTTTTT
3509 GTTTTTGTTTC
1 GTTTTTGTTTC
*
3520 GTTTTTGTTTT
1 GTTTTTGTTTC
3531 GTTTTTGTT
1 GTTTTTGTT
3540 ACGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:3972 original size:31 final size:31
Alignment explanation
Indices: 3937--4072 Score: 146
Period size: 31 Copynumber: 4.3 Consensus size: 31
3927 TTTGTGCATG
**
3937 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
3968 TGGCATGCCACGTGTCACTTTTTTTGGTACACA
1 TGGCATGCCACGTGTCAC--TTTTTGGTACACA
* *** * *
4001 TGGCGTAATATGTGTCACTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* * * *
4032 TGGCGTGCCACATGTCGCTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
4063 TGGCATGCCA
1 TGGCATGCCA
4073 TCATTGGACA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 64 0.73
33 24 0.27
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACACA
Found at i:4017 original size:64 final size:62
Alignment explanation
Indices: 3948--4066 Score: 157
Period size: 64 Copynumber: 1.9 Consensus size: 62
3938 GGCATGCCAC
*
3948 GTGTCACTTTTTGAAACACATGGCATGCCACGTGTCACTTTTTTTGGTACACATGGCGTAATAT
1 GTGTCACTTTTTGAAACACATGGCATGCCACATGTCAC--TTTTTGGTACACATGGCGTAATAT
** * * * *
4012 GTGTCACTTTTTGGTACACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGC
1 GTGTCACTTTTTGAAACACATGGCATGCCACATGTCACTTTTTGGTACACATGGC
4067 ATGCCATCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 16 0.33
64 32 0.67
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (62 bp):
GTGTCACTTTTTGAAACACATGGCATGCCACATGTCACTTTTTGGTACACATGGCGTAATAT
Found at i:4919 original size:17 final size:19
Alignment explanation
Indices: 4899--4936 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
4889 GCCAGCAGCA
4899 CCAGGCCGC-CAGGCC-AG
1 CCAGGCCGCGCAGGCCTAG
4916 CCAGGCCGCGCAGGCCTAG
1 CCAGGCCGCGCAGGCCTAG
4935 CC
1 CC
4937 CGCGCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.16, C:0.47, G:0.34, T:0.03
Consensus pattern (19 bp):
CCAGGCCGCGCAGGCCTAG
Found at i:5091 original size:16 final size:15
Alignment explanation
Indices: 5067--5142 Score: 74
Period size: 16 Copynumber: 5.3 Consensus size: 15
5057 GCCCAAATTT
*
5067 GAAATAAAGGAAAAA
1 GAAAGAAAGGAAAAA
5082 TGAAAGAAAGGAAAAA
1 -GAAAGAAAGGAAAAA
5098 -AAAGAAAGGGAAAAA
1 GAAAGAAA-GGAAAAA
5113 G-AA-AAAGG-AAAA
1 GAAAGAAAGGAAAAA
5125 -AAA-AAAGGAAAAGA
1 GAAAGAAAGGAAAA-A
5139 GAAA
1 GAAA
5143 TATTAGGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
12 11 0.21
13 5 0.09
14 11 0.21
15 12 0.23
16 14 0.26
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (15 bp):
GAAAGAAAGGAAAAA
Found at i:5113 original size:12 final size:12
Alignment explanation
Indices: 5096--5142 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
5086 AGAAAGGAAA
*
5096 AAAAAGAAAGGG
1 AAAAAGAAAAGG
5108 AAAAAGAAAAAGG
1 AAAAAG-AAAAGG
*
5121 AAAAAAAAAAGG
1 AAAAAGAAAAGG
5133 AAAAGAGAAA
1 AAAA-AGAAA
5143 TATTAGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 16 0.53
13 14 0.47
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:5131 original size:26 final size:28
Alignment explanation
Indices: 5088--5142 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 28
5078 AAAATGAAAG
5088 AAAGGAAAAAAAAGAAAGGGAAAA-AGAA
1 AAAGGAAAAAAAAGAAA-GGAAAAGAGAA
5116 AAAGG-AAAAAAA-AAAGGAAAAGAGAA
1 AAAGGAAAAAAAAGAAAGGAAAAGAGAA
5142 A
1 A
5143 TATTAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 6 0.23
26 8 0.31
27 7 0.27
28 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (28 bp):
AAAGGAAAAAAAAGAAAGGAAAAGAGAA
Found at i:6431 original size:12 final size:11
Alignment explanation
Indices: 6374--6430 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
6364 CCCGTTGAGG
6374 AAATGTTTTAT
1 AAATGTTTTAT
* *
6385 TACTGTTTTACAT
1 AAATGTTTT--AT
*
6398 AAATGATTTAT
1 AAATGTTTTAT
6409 AAAATGTTTTGAT
1 -AAATGTTTT-AT
6422 AAATGTTTT
1 AAATGTTTT
6431 GGGTGCATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 9 0.25
12 17 0.47
13 10 0.28
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (11 bp):
AAATGTTTTAT
Found at i:16687 original size:20 final size:21
Alignment explanation
Indices: 16655--16695 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
16645 ATTTGTTTTC
16655 AAAACATGAAAATGGCAACAA
1 AAAACATGAAAATGGCAACAA
16676 AAAACATG-AAATGGCAACAA
1 AAAACATGAAAATGGCAACAA
16696 TGTCAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.10
Consensus pattern (21 bp):
AAAACATGAAAATGGCAACAA
Found at i:19067 original size:17 final size:17
Alignment explanation
Indices: 19045--19077 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19035 ATTATAAACT
19045 GACATTATTGAGCAATG
1 GACATTATTGAGCAATG
*
19062 GACATTGTTGAGCAAT
1 GACATTATTGAGCAAT
19078 ATTAATATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (17 bp):
GACATTATTGAGCAATG
Found at i:19425 original size:91 final size:91
Alignment explanation
Indices: 19270--19449 Score: 342
Period size: 91 Copynumber: 2.0 Consensus size: 91
19260 GTGTAGGTCT
19270 GTTCTGTTTCGGTGTTCTCCCGGGCTACACGTGAGGGGGCGTGTTAAAGTGGTAATATCCCACAT
1 GTTCTGTTTCGGTGTTCTCCCGGGCTACACGTGAGGGGGCGTGTTAAAGTGGTAATATCCCACAT
19335 TGGTTATGTTTGACATGACTGGGTTC
66 TGGTTATGTTTGACATGACTGGGTTC
* *
19361 GTTCTGTTTCGGTGTTCTCCCGGGCTACATGTGAGGGGGCGTGTTAAAGTGGTAATATCTCACAT
1 GTTCTGTTTCGGTGTTCTCCCGGGCTACACGTGAGGGGGCGTGTTAAAGTGGTAATATCCCACAT
19426 TGGTTATGTTTGACATGACTGGGT
66 TGGTTATGTTTGACATGACTGGGT
19450 GCTAATATCC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (91 bp):
GTTCTGTTTCGGTGTTCTCCCGGGCTACACGTGAGGGGGCGTGTTAAAGTGGTAATATCCCACAT
TGGTTATGTTTGACATGACTGGGTTC
Found at i:26309 original size:331 final size:331
Alignment explanation
Indices: 25707--26365 Score: 1183
Period size: 331 Copynumber: 2.0 Consensus size: 331
25697 TAGGACTCTG
* *
25707 CCCGCGCTTCGCCGCGGGCGGGTGTCTGTAACTTGTTAATGGTGAAGGGATTTGTTGGCATTGCA
1 CCCGCGCTTCGCCGCGGACGGGTGTCTGTAACTTGTTAATGGTGAAGAGATTTGTTGGCATTGCA
** *
25772 ATAGCAATTGTTGGATTGTTTAAAAAGAAGTCAATTTTTTGGCACTATTGAGGTTCTGCGCAGTT
66 ATAGCAATTGTTGGATTGTCAAAAAAGAAGTCAATTTTTTAGCACTATTGAGGTTCTGCGCAGTT
25837 GTTGAAGCATGACTCGAGTATAGAAATCAGGGTGATGCTTGTGTAATAATGGAAGAAAGGTTTGA
131 GTTGAAGCATGACTCGAGTATAGAAATCAGGGTGATGCTTGTGTAATAATGGAAGAAAGGTTTGA
25902 GTGGATGGATTTATTCAAAGATATTTGTTGATCATTGATTATGATGAATACTTACAATGCACAAG
196 GTGGATGGATTTATTCAAAGATATTTGTTGATCATTGATTATGATGAATACTTACAATGCACAAG
*
25967 GAGATTTCGGTGTCTTCGATGAACATGGTGCAAGATATAAGGTGCACATGAATATAATTGATTAG
261 GAGATTTCGGTGTCTTCAATGAACATGGTGCAAGATATAAGGTGCACATGAATATAATTGATTAG
26032 ACGTTA
326 ACGTTA
* *
26038 CCCGCGCTTCGCCGCGGACGGGTGTCTGTAACTTGTTAATGGTGAAGAGATTTGTTGGTATTGGA
1 CCCGCGCTTCGCCGCGGACGGGTGTCTGTAACTTGTTAATGGTGAAGAGATTTGTTGGCATTGCA
*
26103 ATAGCAATTGTTGGATTGTCAAAAAAGAAGTCAATTTTTTAGCACTATTGAGGTTCTGCGCGGTT
66 ATAGCAATTGTTGGATTGTCAAAAAAGAAGTCAATTTTTTAGCACTATTGAGGTTCTGCGCAGTT
* *
26168 GTTGAAGCGTGACTCGAGTATAGAAATCAGGTTGATGCTTGTGTAATAATGGAAGAAAGGTTTGA
131 GTTGAAGCATGACTCGAGTATAGAAATCAGGGTGATGCTTGTGTAATAATGGAAGAAAGGTTTGA
* *
26233 GTGGATGGATTTATTTAAAGATCTTTGTTGATCATTGATTATGATGAATACTTACAATGCACAAG
196 GTGGATGGATTTATTCAAAGATATTTGTTGATCATTGATTATGATGAATACTTACAATGCACAAG
* *
26298 GAGATTTCGGTGTCTTTAATGAACATGGTGCAAGATATAAGGTGCACATGAATATAATTTATTAG
261 GAGATTTCGGTGTCTTCAATGAACATGGTGCAAGATATAAGGTGCACATGAATATAATTGATTAG
26363 ACG
326 ACG
26366 GTGGTCAAGT
Statistics
Matches: 313, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
331 313 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (331 bp):
CCCGCGCTTCGCCGCGGACGGGTGTCTGTAACTTGTTAATGGTGAAGAGATTTGTTGGCATTGCA
ATAGCAATTGTTGGATTGTCAAAAAAGAAGTCAATTTTTTAGCACTATTGAGGTTCTGCGCAGTT
GTTGAAGCATGACTCGAGTATAGAAATCAGGGTGATGCTTGTGTAATAATGGAAGAAAGGTTTGA
GTGGATGGATTTATTCAAAGATATTTGTTGATCATTGATTATGATGAATACTTACAATGCACAAG
GAGATTTCGGTGTCTTCAATGAACATGGTGCAAGATATAAGGTGCACATGAATATAATTGATTAG
ACGTTA
Found at i:32589 original size:74 final size:73
Alignment explanation
Indices: 32468--32614 Score: 267
Period size: 74 Copynumber: 2.0 Consensus size: 73
32458 CCTACCAAAA
*
32468 AAAACTTTCAGAAAATTATTCCCTTCAAGACTAACCATATTATTTTAGGACTTACCTATAAAAGT
1 AAAACTTGCAGAAAATTATTCCCTTCAAGACTAACCATATTATTTTA-GACTTACCTATAAAAGT
32533 TTATTTCTT
65 TTATTTCTT
*
32542 AAAACTTGCAGAAAATTATTCTCTTCAAGACTAACCATATTATTTTAGACTTACCTATAAAAGTT
1 AAAACTTGCAGAAAATTATTCCCTTCAAGACTAACCATATTATTTTAGACTTACCTATAAAAGTT
32607 TATTTCTT
66 TATTTCTT
32615 TACTCGTATC
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 26 0.37
74 45 0.63
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (73 bp):
AAAACTTGCAGAAAATTATTCCCTTCAAGACTAACCATATTATTTTAGACTTACCTATAAAAGTT
TATTTCTT
Found at i:34111 original size:4 final size:4
Alignment explanation
Indices: 34102--34132 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
34092 CAAATATTCA
34102 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
34133 TATATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:37713 original size:34 final size:34
Alignment explanation
Indices: 37670--37736 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
37660 AGATCTCACT
*
37670 GGGTTTGTTTGTTGGCTCATAGATTAGCGTTTCG
1 GGGTTTGTTTGTTGGCTCATAAATTAGCGTTTCG
37704 GGGTTTGTTTGTTGGCTCATAAATTAGCGTTTC
1 GGGTTTGTTTGTTGGCTCATAAATTAGCGTTTC
37737 AGTAATGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.13, C:0.12, G:0.30, T:0.45
Consensus pattern (34 bp):
GGGTTTGTTTGTTGGCTCATAAATTAGCGTTTCG
Found at i:38063 original size:13 final size:13
Alignment explanation
Indices: 38045--38075 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
38035 TTTGGAATTC
38045 TAAATAATATTTA
1 TAAATAATATTTA
38058 TAAATAATATTTA
1 TAAATAATATTTA
38071 -AAATA
1 TAAATA
38076 TTGAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAATAATATTTA
Found at i:38506 original size:6 final size:6
Alignment explanation
Indices: 38489--38518 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
38479 AGTTACAAGT
*
38489 AAAAGA AGAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
38519 CGATTTAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:40126 original size:21 final size:21
Alignment explanation
Indices: 40100--40140 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
40090 TGCTAGAAGT
40100 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
40121 TCATTGGAGCAAGTTCCAAG
1 TCATTGGAGCAAGTTCCAAG
40141 ATCCTGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:40259 original size:179 final size:179
Alignment explanation
Indices: 39959--40319 Score: 722
Period size: 179 Copynumber: 2.0 Consensus size: 179
39949 GCTTGGAAAA
39959 AAGATCCTGAATCATTATCATTGTTAGTGCAATGCTGATGCGCCAAGGACTCATCATGGTCTAGA
1 AAGATCCTGAATCATTATCATTGTTAGTGCAATGCTGATGCGCCAAGGACTCATCATGGTCTAGA
40024 AGAGCACAATGCAGATCATGGAGGGAATGTGCATATGCGGCAAGGAGGCTTGAAGAAGCTTGAAG
66 AGAGCACAATGCAGATCATGGAGGGAATGTGCATATGCGGCAAGGAGGCTTGAAGAAGCTTGAAG
40089 ATGCTAGAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAAGTTCC
131 ATGCTAGAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAAGTTCC
40138 AAGATCCTGAATCATTATCATTGTTAGTGCAATGCTGATGCGCCAAGGACTCATCATGGTCTAGA
1 AAGATCCTGAATCATTATCATTGTTAGTGCAATGCTGATGCGCCAAGGACTCATCATGGTCTAGA
40203 AGAGCACAATGCAGATCATGGAGGGAATGTGCATATGCGGCAAGGAGGCTTGAAGAAGCTTGAAG
66 AGAGCACAATGCAGATCATGGAGGGAATGTGCATATGCGGCAAGGAGGCTTGAAGAAGCTTGAAG
40268 ATGCTAGAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAAGTTCC
131 ATGCTAGAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAAGTTCC
40317 AAG
1 AAG
40320 CTCATTGGAG
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 182 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (179 bp):
AAGATCCTGAATCATTATCATTGTTAGTGCAATGCTGATGCGCCAAGGACTCATCATGGTCTAGA
AGAGCACAATGCAGATCATGGAGGGAATGTGCATATGCGGCAAGGAGGCTTGAAGAAGCTTGAAG
ATGCTAGAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAAGTTCC
Found at i:40305 original size:21 final size:21
Alignment explanation
Indices: 40279--40391 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
40269 TGCTAGAAGT
40279 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
40300 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
40321 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
40342 TCATTGGAG-AATGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
40363 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
40384 TCATTGGA
1 TCATTGGA
40392 AATGCCTAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 1 0.01
21 83 0.99
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.