Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017715.1 Corchorus olitorius cultivar O-4 contig17748, 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: 23509
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--42 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 CAACTTACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:546 original size:21 final size:22
Alignment explanation
Indices: 521--574 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
511 ATTACACTAT
* *
521 TTTTTATAACC-TCCTCATGAAA
1 TTTTAATAACCTTCCT-ATAAAA
* *
543 TTTTGATTACCTTCCTATAAAA
1 TTTTAATAACCTTCCTATAAAA
565 TTTTAATAAC
1 TTTTAATAAC
575 GATACTACGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (22 bp):
TTTTAATAACCTTCCTATAAAA
Found at i:816 original size:22 final size:22
Alignment explanation
Indices: 791--1096 Score: 125
Period size: 22 Copynumber: 14.1 Consensus size: 22
781 GAATTGTTAG
*
791 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
813 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
835 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
857 TAAAC-CTTCCTATAAAATTTTGA
1 TAATCAC--ACTATGAAATTTTGA
* * * *
880 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
* * * *
903 TAACCTC-CTTATTAAATATTG-
1 TAATCACAC-TATGAAATTTTGA
*
924 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
941 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
963 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
985 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
1007 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* *
1029 TAA-CCCTCTTATGAAATTTTGGA
1 TAATCACAC-TATGAAATTTT-GA
*
1052 -AA-CTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
1073 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
1095 TA
1 TA
1097 TCCGCCCTGA
Statistics
Matches: 221, Mismatches: 44, Indels: 38
0.73 0.15 0.13
Matches are distributed among these distances:
16 7 0.03
17 2 0.01
18 1 0.00
19 2 0.01
21 10 0.05
22 159 0.72
23 36 0.16
24 3 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:1020 original size:44 final size:44
Alignment explanation
Indices: 802--1095 Score: 187
Period size: 44 Copynumber: 6.8 Consensus size: 44
792 AATCACACTC
* * * * * * *
802 TGAAATTTTGATAATCACACTATGAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATCTACAT-ACTA
* * ** * *
846 TGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCCCTATGAAATTTTGATCTACAT-ACTA
* * * *
892 TAAAATTTTGATAACCTCCTTATTAAATATTGA--T--A-ACTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATCTACATACTA
* ** * * *
931 -CAAATTTTGATAACCTCCCTATGATTTTTTGAT-AACCTCATTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATCTACAT-ACTA
* *
974 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATCTACATACTA
* *
1018 TGAAATTTTGATAACC-CTCTTATGAAATTTTGGAAACTA-A-ACTA
1 TGAAATTTTGATAACCTC-CCTATGAAATTTT-G-ATCTACATACTA
* *
1062 TGAAATTTTGATAACCTTCATATGAAATTTTGAT
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGAT
1096 ATCCGCCCTG
Statistics
Matches: 198, Mismatches: 39, Indels: 28
0.75 0.15 0.11
Matches are distributed among these distances:
38 26 0.13
39 3 0.02
42 1 0.01
43 5 0.03
44 101 0.51
45 38 0.19
46 24 0.12
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (44 bp):
TGAAATTTTGATAACCTCCCTATGAAATTTTGATCTACATACTA
Found at i:1063 original size:66 final size:66
Alignment explanation
Indices: 802--1096 Score: 207
Period size: 66 Copynumber: 4.5 Consensus size: 66
792 AATCACACTC
* * ** *
802 TGAAATTTTGATAATCACAC-TATGAAATTGTGATAACCTCGCTATGAAATTTTGAT-AAACCTT
1 TGAAATTTTGATAA-CATACATATGAAATTTTGATAACCTCATTATGAAATTTTG-TGAAA-CTA
*
865 CCTA
63 ACTA
* * * * * * * *
869 TAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATTAAA-TAT-TG--A-TAAC
1 TGAAATTTTGAT-AACATACATATGAAATTTTGATAACCTCATTATGAAATTTTGTGAAACTAAC
929 TA
65 TA
* * * * ** * * **
931 -CAAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCT
1 TGAAATTTTGATAACATACATATGAAATTTTGATAACCTCATTATGAAATTTTGTGAAACTAACT
995 A
66 A
*
996 TGAAATTTTGATCTACATAC-TATGAAATTTTGATAACCCTC-TTATGAAATTTTG-GAAACTAA
1 TGAAATTTTGAT-AACATACATATGAAATTTTGATAA-CCTCATTATGAAATTTTGTGAAACT-A
1058 ACTA
63 ACTA
* *
1062 TGAAATTTTGATAACCTTCATATGAAATTTTGATA
1 TGAAATTTTGATAACATACATATGAAATTTTGATA
1097 TCCGCCCTGA
Statistics
Matches: 179, Mismatches: 36, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
60 32 0.18
61 12 0.07
62 5 0.03
64 1 0.01
65 13 0.07
66 67 0.37
67 23 0.13
68 26 0.15
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (66 bp):
TGAAATTTTGATAACATACATATGAAATTTTGATAACCTCATTATGAAATTTTGTGAAACTAACT
A
Found at i:1246 original size:22 final size:22
Alignment explanation
Indices: 1221--1639 Score: 153
Period size: 22 Copynumber: 18.9 Consensus size: 22
1211 AATTACATTT
* *
1221 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
1243 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
1265 TAAAATTTTGTTGACCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
1287 TGAAATTTTGATAA-TTACGT-TA
1 TGAAATTTTGATAACCT-C-TCTA
* * *
1309 TGCAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
* * **
1331 TTAAATATTGATAACAACATC-A
1 TGAAATTTTGATAACCTC-TCTA
*
1353 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
* *
1375 T-AAATTTTGATAATCTGATCGCTA
1 TGAAATTTTGATAA-C--CTCTCTA
*** * *
1399 TGAAATTTCCTTAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
1421 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
1441 TCAAATTTTGGTACTCCT-TATAAAA
1 TGAAATTTTGATA-ACCTCTCT---A
*
1466 TTGAGACTTTT-ATAACCT-TCATA
1 -TGA-AATTTTGATAACCTCTC-TA
* *
1489 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
** * ** *
1511 AAAAATATTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
** * *
1533 CAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
*
1555 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
1577 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* * *
1599 TGAAACTCTT-ATAACTTCGCTA
1 TGAAA-TTTTGATAACCTCTCTA
* *
1621 TGACATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
1640 TTGATAACCT
Statistics
Matches: 286, Mismatches: 83, Indels: 56
0.67 0.20 0.13
Matches are distributed among these distances:
20 8 0.03
21 35 0.12
22 205 0.72
23 9 0.03
24 5 0.02
25 14 0.05
26 5 0.02
27 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:1602 original size:44 final size:43
Alignment explanation
Indices: 1221--1839 Score: 126
Period size: 44 Copynumber: 14.2 Consensus size: 43
1211 AATTACATTT
* * ** *
1221 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCACACTATGAAATATTGATAACCTC-CTA
* * * * * * *
1265 TAAAATTTTGTTGACCACTCTATGAAATTTTGATAA-TTACGTTA
1 TGAAATTTTGATAACCACACTATGAAATATTGATAACCT-C-CTA
* * * * * ** *
1309 TGCAATTTTGATAACCTCGCTTTTAAATATTGATAACAACATCA
1 TGAAATTTTGATAACCACACTATGAAATATTGATAACCTCCT-A
** * *
1353 TGAAATTTTGATAATCTTC-CTAT-AAATTTTGATAATCTGATCGCTA
1 TGAAATTTTGATAA-CCACACTATGAAATATTGATAA-C--CTC-CTA
*** * * * *
1399 TGAAATTTCCTTAATCACTCTATGAGAT-TTGATAACCTTCTA
1 TGAAATTTTGATAACCACACTATGAAATATTGATAACCTCCTA
* * * * ** * * *
1441 TCAAATTTTGGTACTCCTTATAAAATTGAGACT-TTTATAACCTTCATA
1 TGAAATTTTGATA-ACC--ACACTA-TGA-AATATTGATAACC-TCCTA
** **
1489 TGAAATTTTGATAACCACACTAAAAAATATTGATAACAACACTA
1 TGAAATTTTGATAACCACACTATGAAATATTGATAACCTC-CTA
** * * *
1533 CAAAATTTTGATAACCTCCCCATGAAATATT-AGTAACCTCCTTA
1 TGAAATTTTGATAACCACACTATGAAATATTGA-TAACCTCC-TA
* * *
1577 TGAAATTTTGTTAACCACACTATGAAACTCTT-ATAACTTCGCTA
1 TGAAATTTTGATAACCACACTATGAAA-TATTGATAACCTC-CTA
* * * *
1621 TGACATTTTGAT----A-A-TCT---CT-TTGATAACCTTTCTA
1 TGAAATTTTGATAACCACACTATGAAATATTGATAACC-TCCTA
* * * * * *
1655 TAAAATTGTGCTTACCACACTATGAAAT-TTCAATAACATTCCTA
1 TGAAATTTTGATAACCACACTATGAAATATT-GATAAC-CTCCTA
* * * * *
1699 CGAAATTTTAATAACCTGATC-CTATGAAATTTTGATAACCACACTG
1 TGAAATTTTGATAACC--A-CACTATGAAATATTGATAACCTC-CTA
** * * **
1745 TGAAATTTTGATAACCTTA-TGATGAAATTTTGATAACTTTTATA
1 TGAAATTTTGATAACCACACT-ATGAAATATTGATAAC-CTCCTA
* * * * *
1789 TGAAAGTTTGGTGACCACACTATGGAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACCACACTATGAAATATTGATAACCTCCT-A
1833 TGAAATT
1 TGAAATT
1840 ATAATAATCA
Statistics
Matches: 405, Mismatches: 125, Indels: 90
0.65 0.20 0.15
Matches are distributed among these distances:
33 2 0.00
34 17 0.04
35 1 0.00
38 3 0.01
39 2 0.00
40 3 0.01
42 12 0.03
43 26 0.06
44 231 0.57
45 17 0.04
46 59 0.15
47 18 0.04
48 14 0.03
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (43 bp):
TGAAATTTTGATAACCACACTATGAAATATTGATAACCTCCTA
Found at i:1727 original size:24 final size:22
Alignment explanation
Indices: 1674--1870 Score: 87
Period size: 22 Copynumber: 8.9 Consensus size: 22
1664 GCTTACCACA
* *
1674 CTATGAAATTTCAATAACATTC
1 CTATGAAATTTTAATAACCTTC
*
1696 CTACGAAATTTTAATAACCTGATC
1 CTATGAAATTTTAATAACCT--TC
* *
1720 CTATGAAATTTTGATAACC-AC
1 CTATGAAATTTTAATAACCTTC
* *
1741 ACTGTGAAATTTTGATAACCTT-
1 -CTATGAAATTTTAATAACCTTC
* * * *
1763 ATGATGAAATTTTGATAACTTTT
1 CT-ATGAAATTTTAATAACCTTC
* * ** * *
1786 ATATGAAAGTTTGGTGACC-AC
1 CTATGAAATTTTAATAACCTTC
* *
1807 ACTATGGAATTTTGATAACC-TC
1 -CTATGAAATTTTAATAACCTTC
* * *
1829 CTCATGAAATTATAATAATCATC
1 CT-ATGAAATTTTAATAACCTTC
* * *
1852 TTATGAAATTCTGATAACC
1 CTATGAAATTTTAATAACC
1871 ACACAGAGAC
Statistics
Matches: 135, Mismatches: 31, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
21 4 0.03
22 107 0.79
23 5 0.04
24 19 0.14
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCTTC
Found at i:1857 original size:66 final size:65
Alignment explanation
Indices: 1668--1874 Score: 184
Period size: 66 Copynumber: 3.1 Consensus size: 65
1658 AATTGTGCTT
** * * * * *
1668 ACCACACTATGAAATTTCAATAACATTCCTACGAAATTTTAATAACCTGATCCTATGAAATTTTG
1 ACCACACTATGAAATTTTGATAAC-CTCCTATGAAATTTTAATAA--TCATCTTATGAAAGTTTG
1733 ATA
63 ATA
* ** * * * *
1736 ACCACACTGTGAAATTTTGATAACCTTATGATGAAATTTTGATAA-CTTTTATATGAAAGTTTGG
1 ACCACACTATGAAATTTTGATAACCTCCT-ATGAAATTTTAATAATCATCT-TATGAAAGTTTGA
*
1800 TG
64 TA
* *
1802 ACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAATCATCTTATGAAA-TTCTGA
1 ACCACACTATGAAATTTTGATAACCTCCT-ATGAAATTTTAATAATCATCTTATGAAAGTT-TGA
1866 TA
64 TA
1868 ACCACAC
1 ACCACAC
1875 AGAGACAAGA
Statistics
Matches: 109, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
65 3 0.03
66 67 0.61
67 5 0.05
68 34 0.31
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (65 bp):
ACCACACTATGAAATTTTGATAACCTCCTATGAAATTTTAATAATCATCTTATGAAAGTTTGATA
Found at i:11573 original size:22 final size:22
Alignment explanation
Indices: 11548--11591 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11538 CATATCCCAA
11548 AGATAGAGCTGACATTGGACCT
1 AGATAGAGCTGACATTGGACCT
11570 AGATAGAGCTGACATTGGACCT
1 AGATAGAGCTGACATTGGACCT
11592 TGTATCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (22 bp):
AGATAGAGCTGACATTGGACCT
Found at i:12658 original size:95 final size:95
Alignment explanation
Indices: 12480--12658 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 95
12470 TGAAAACATT
* * * *
12480 GTTTGAAAGGGGAGGAGATGGATTTGGCTTTCAAGCCAAACCCTAAACGAGGGCTGATCGGCGCC
1 GTTTGAAAGGGGAAGAGAGGGATTTGGCTTTCAAGCCAAACCCTAAACGAGGGCTAATCGACGCC
*
12545 GGAGAAGGGAGCAGAGGCAGCTGACATGGA
66 GGAGAAGGAAGCAGAGGCAGCTGACATGGA
* * ** *
12575 GTTTG-AAGGAGGAAGAGAGGGCTTTGGCTTTGCAAGCCCAACCCTCGACGATGGCTAATCGACG
1 GTTTGAAAGG-GGAAGAGAGGGATTTGGCTTT-CAAGCCAAACCCTAAACGAGGGCTAATCGACG
*
12639 TCGGAGAAGGAAGCA-AGGCA
64 CCGGAGAAGGAAGCAGAGGCA
12659 CGACTAAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
94 4 0.06
95 28 0.39
96 39 0.55
ACGTcount: A:0.28, C:0.19, G:0.36, T:0.16
Consensus pattern (95 bp):
GTTTGAAAGGGGAAGAGAGGGATTTGGCTTTCAAGCCAAACCCTAAACGAGGGCTAATCGACGCC
GGAGAAGGAAGCAGAGGCAGCTGACATGGA
Found at i:13391 original size:33 final size:33
Alignment explanation
Indices: 13349--13465 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
13339 GACCGGATCG
* *
13349 CGCCTCCCCATATGGTGAGGCGCCTCCTGGGGA
1 CGCCTCCCCATATGGTCAGGCGCCCCCTGGGGA
13382 CGCCTCCCCATATGGTCAGGCGCCCCCTGGGGA
1 CGCCTCCCCATATGGTCAGGCGCCCCCTGGGGA
* * * * *
13415 GGCCTCGCCATATGGTCAGGTGCCCCCTAGAGA
1 CGCCTCCCCATATGGTCAGGCGCCCCCTGGGGA
*
13448 CGCCTCGCCATATGGTCA
1 CGCCTCCCCATATGGTCA
13466 AGCTTGGACA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.15, C:0.38, G:0.30, T:0.18
Consensus pattern (33 bp):
CGCCTCCCCATATGGTCAGGCGCCCCCTGGGGA
Found at i:16517 original size:3 final size:3
Alignment explanation
Indices: 16509--16565 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
16499 TATATTAATC
** *
16509 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACC GTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16557 ATT ATT ATT
1 ATT ATT ATT
16566 GTTCTTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:19168 original size:14 final size:13
Alignment explanation
Indices: 19106--19170 Score: 87
Period size: 14 Copynumber: 4.8 Consensus size: 13
19096 ATAAAGGATT
19106 TTTTCAAAAATGA
1 TTTTCAAAAATGA
19119 TTTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
19133 TTTTCAAGAAATGA
1 TTTTCAA-AAATGA
19147 TTTTCAAAAATGA
1 TTTTCAAAAATGA
19160 GTTTTCAAAAA
1 -TTTTCAAAAA
19171 GGTTTTGAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.31
14 31 0.65
15 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:19434 original size:6 final size:6
Alignment explanation
Indices: 19419--19463 Score: 81
Period size: 6 Copynumber: 7.3 Consensus size: 6
19409 TGAATAAGAA
19419 AAAAAGG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
19464 GATTGTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:19840 original size:6 final size:6
Alignment explanation
Indices: 19829--19876 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
19819 GAATCAATCT
* *
19829 AAAGAA AAAGAA GAAGAA AAAGAA AAAG-C AAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
19876 A
1 A
19877 GAAAAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:19889 original size:16 final size:17
Alignment explanation
Indices: 19829--19882 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
19819 GAATCAATCT
*
19829 AAAGAAAAAGAAGAAGAA
1 AAAGAAAAAGCA-AAGAA
19847 AAAGAAAAAGCAAAGAA
1 AAAGAAAAAGCAAAGAA
19864 AAAGAAAAAG-AAAGAA
1 AAAGAAAAAGCAAAGAA
19880 AAA
1 AAA
19883 TCAAAAGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 9 0.26
17 15 0.43
18 11 0.31
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGCAAAGAA
Found at i:19893 original size:17 final size:16
Alignment explanation
Indices: 19842--19893 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
19832 GAAAAAGAAG
*
19842 AAGAAAAAGAAAAAGCA
1 AAGAAAAA-AAAAAGGA
19859 AAGAAAAAGAAAAA-GA
1 AAGAAAAA-AAAAAGGA
*
19875 AAGAAAAATCAAAAGGA
1 AAGAAAAA-AAAAAGGA
19892 AA
1 AA
19894 AGGTTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (16 bp):
AAGAAAAAAAAAAGGA
Found at i:20161 original size:87 final size:87
Alignment explanation
Indices: 20015--20270 Score: 415
Period size: 87 Copynumber: 2.9 Consensus size: 87
20005 TGTTTGAAGG
20015 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
1 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
20080 TTGGAGGAAGATTTGGGAAATA
66 TTGGAGGAAGATTTGGGAAATA
20102 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
1 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
* *
20167 TTGGAGGAAAATTTGAGAAATA
66 TTGGAGGAAGATTTGGGAAATA
* * * * *
20189 TTTCTCAAGGTGGGAAGCTGATCCA-AAACCATCAATTGAGTTGGGAATATCAATACATGATCAA
1 TTTCTTAAGATGAGAAACTGATCCAGAAA-CATCAATTGAGTTGGGAATATCAATGCATGATCAA
* *
20253 ATTGGAAGAAGGTTTGGG
65 ATTGGAGGAAGATTTGGG
20271 GCATCAATCG
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
86 3 0.02
87 154 0.98
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.27
Consensus pattern (87 bp):
TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAAA
TTGGAGGAAGATTTGGGAAATA
Found at i:21727 original size:37 final size:37
Alignment explanation
Indices: 21044--21720 Score: 636
Period size: 37 Copynumber: 18.4 Consensus size: 37
21034 TTCAAGATTT
21044 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * * *
21081 TGTTTAGGTGT-TTCATAAAAAT-CTTGTTCAAGATTCC
1 TGTTTAGGTGTCTT-AT-CAAATCCTTATTTAAGGTCCC
*
21118 TGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* *
21155 TGTATAGGTGTCTTATTAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
*
21192 TGTTTAAGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* ** * * *
21229 TGTTTAGGTGTCTCATCGAAAT-CTGGTTCAAGATCCT
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* * * * *
21266 TGTTTAGGTGTCTCATCAAAAT-CTTGTTCAAGATTCC
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* *
21303 TGTTTAGATTTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * * *
21340 TGTTTAGATGTCTCATCAAAACCTTGTTTAAGATCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * *
21377 TATTTAGGTTTCTTGTCAAATCCTTATTTAAGGTTCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * * **
21414 TATTCAGGTGTC--ATCAAAGT-CTTGTTCAACATCCC
1 TGTTTAGGTGTCTTATCAAA-TCCTTATTTAAGGTCCC
* *
21449 TGTTTAGGTTTCTTATCAAAATCCTTATTTAAGGTCTC
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* * *
21487 TATTTAGGTGTCTCATCAAAATCCTTATTTAAGATCCC
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* *
21525 TG-TTAGGTTTCTTATCAAATCCTTATTTAAGGTCCT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * * * * * *
21561 TATTTATGCGTCTCATCAAAACCTTGTTCAAGGTCCT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * *
21598 TGTTT-GGATGTCTCATCAAAACCTTGTTTAAGGTCCC
1 TGTTTAGG-TGTCTTATCAAATCCTTATTTAAGGTCCC
* * * * * * *
21635 TTTTTAGCTGTCTTATCAAA-CCTTGTTCAAGATTCT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* *
21671 TGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
21708 TGTTTAGGTGTCT
1 TGTTTAGGTGTCT
21721 CTTCAAAATC
Statistics
Matches: 523, Mismatches: 102, Indels: 30
0.80 0.16 0.05
Matches are distributed among these distances:
35 24 0.05
36 60 0.11
37 381 0.73
38 58 0.11
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (37 bp):
TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
Found at i:21894 original size:54 final size:53
Alignment explanation
Indices: 21827--22194 Score: 479
Period size: 54 Copynumber: 6.8 Consensus size: 53
21817 TTTCTCTAGA
* *
21827 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTTAGAGATCT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * *
21881 AAGTTGATCTTAAGATGACCCAGTGTGGTTTTTCATGGAAATTTTCAGAGATCT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
21935 AAGTTGATCTTAAGTTGACTCAGTGTGATCTTTCATAGAAGTTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGAC-CAGTGTGGTCTTTCATAGAAG-TTTTCAGAGATCT
*
21990 AAGTTGATCTTAAGATGACCAGTGTGGTCTTTCATAGAAATTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
22043 AAGTTGATCTTAAGATGACCTAGTGTGGTCTTTCATAGAAGCTTTT-AAAGGTCT
1 AAGTTGATCTTAAGATGACC-AGTGTGGTCTTTCATAGAAG-TTTTCAGAGATCT
* * * * *
22097 AAGTTGATCTTCAGATGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * *
22151 AAGTTGATTTTAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTC-TTTCATAGAAGTTT
22195 ACGATGATCA
Statistics
Matches: 280, Mismatches: 27, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
53 38 0.14
54 200 0.71
55 42 0.15
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (53 bp):
AAGTTGATCTTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
Found at i:22016 original size:108 final size:108
Alignment explanation
Indices: 21827--22194 Score: 537
Period size: 108 Copynumber: 3.4 Consensus size: 108
21817 TTTCTCTAGA
21827 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTTAGAGATCTAAGTTGATCTT
1 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTTAGAGATCTAAGTTGATCTT
* *
21892 AAGATGACCCAGTGTGGTTTTTCATGGAAATTTTCAGAGATCT
66 AAGATGACCCAGTGTGGTCTTTCATAGAAATTTTCAGAGATCT
*
21935 AAGTTGATCTTAAGTTGA-CTCAGTGTGATCTTTCATAGAAGTTTTTCAGAGATCTAAGTTGATC
1 AAGTTGATCTTAAGTTGATC-CAGTGTGGTCTTTCATAGAAGTTTTT-AGAGATCTAAGTTGATC
21999 TTAAGATGA-CCAGTGTGGTCTTTCATAGAAATTTTCAGAGATCT
64 TTAAGATGACCCAGTGTGGTCTTTCATAGAAATTTTCAGAGATCT
* * * *
22043 AAGTTGATCTTAAGATGA-CCTAGTGTGGTCTTTCATAGAAGCTTTTAAAGGTCTAAGTTGATCT
1 AAGTTGATCTTAAGTTGATCC-AGTGTGGTCTTTCATAGAAGTTTTTAGAGATCTAAGTTGATCT
* * * * * *
22107 TCAGATGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
65 TAAGATGACCCAGTGTGGTCTTTCATAGAAATTTTCAGAGATCT
* *
22151 AAGTTGATTTTAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTT
1 AAGTTGATCTTAAGTTGATCCAGTGTGGTC-TTTCATAGAAGTTT
22195 ACGATGATCA
Statistics
Matches: 236, Mismatches: 18, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
107 25 0.11
108 179 0.76
109 32 0.14
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (108 bp):
AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTTAGAGATCTAAGTTGATCTT
AAGATGACCCAGTGTGGTCTTTCATAGAAATTTTCAGAGATCT
Found at i:22490 original size:7 final size:7
Alignment explanation
Indices: 22476--22615 Score: 181
Period size: 7 Copynumber: 20.0 Consensus size: 7
22466 GCATTTCATT
22476 ACTCAAA
1 ACTCAAA
*
22483 ATTCAAA
1 ACTCAAA
*
22490 ATTCAAA
1 ACTCAAA
*
22497 ATTCAAA
1 ACTCAAA
*
22504 ATTCAAA
1 ACTCAAA
*
22511 ATTCAAA
1 ACTCAAA
*
22518 ATTCAAA
1 ACTCAAA
*
22525 ATTCAAA
1 ACTCAAA
*
22532 ATTCAAA
1 ACTCAAA
22539 ACTCAAA
1 ACTCAAA
22546 ACTCAAA
1 ACTCAAA
22553 ACTCAAA
1 ACTCAAA
22560 ACTCAAA
1 ACTCAAA
22567 ACTCAAA
1 ACTCAAA
22574 ACTCAAA
1 ACTCAAA
22581 ACTCAAA
1 ACTCAAA
22588 ACTCAAA
1 ACTCAAA
**
22595 ACTCATG
1 ACTCAAA
22602 ACTCAAA
1 ACTCAAA
*
22609 AATCAAA
1 ACTCAAA
22616 TTTCAAAACC
Statistics
Matches: 126, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 126 1.00
ACGTcount: A:0.56, C:0.22, G:0.01, T:0.21
Consensus pattern (7 bp):
ACTCAAA
Done.