Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015162.1 Corchorus olitorius cultivar O-4 contig15195, 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: 66195
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:534 original size:2 final size:2
Alignment explanation
Indices: 527--556 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
517 TCATTACTAG
527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
557 AATTGAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:804 original size:20 final size:21
Alignment explanation
Indices: 779--819 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
769 TTTGAATGAT
779 GTTGGAAAACCAA-CTTTGCA
1 GTTGGAAAACCAACCTTTGCA
* *
799 GTTGGAGAAGCAACCTTTGCA
1 GTTGGAAAACCAACCTTTGCA
820 CGAATCCGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (21 bp):
GTTGGAAAACCAACCTTTGCA
Found at i:9063 original size:13 final size:13
Alignment explanation
Indices: 9045--9070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9035 GCATCTTGGC
9045 TCAATGGTAAGGT
1 TCAATGGTAAGGT
9058 TCAATGGTAAGGT
1 TCAATGGTAAGGT
9071 GCATGCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
TCAATGGTAAGGT
Found at i:10436 original size:18 final size:18
Alignment explanation
Indices: 10413--10450 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
10403 TGAAATTTAT
10413 TAATTATTTATTA-AATAA
1 TAATTATTT-TTAGAATAA
10431 TAATTATTTTTAGAATAA
1 TAATTATTTTTAGAATAA
10449 TA
1 TA
10451 TATACTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATTATTTTTAGAATAA
Found at i:23005 original size:36 final size:36
Alignment explanation
Indices: 22914--23005 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
22904 GATTGACCCG
* *
22914 ATCAACGGATGACGTGGCAAGTTGACTCGGTCAACA
1 ATCAACGGATGACGTGGCAGGTTGACTCAGTCAACA
*
22950 ATCAACGGATGATGTGGCAGGTTGACT-AGTCAACA
1 ATCAACGGATGACGTGGCAGGTTGACTCAGTCAACA
*
22985 GTCAACTGGATGACGTGGCAG
1 ATCAAC-GGATGACGTGGCAG
23006 CAGAGGATTG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
35 12 0.24
36 38 0.76
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (36 bp):
ATCAACGGATGACGTGGCAGGTTGACTCAGTCAACA
Found at i:25279 original size:16 final size:16
Alignment explanation
Indices: 25260--25295 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
25250 AGATTCTTTG
25260 TTGGTGTTGATCAATT
1 TTGGTGTTGATCAATT
25276 TTGGTGTTGATCAATT
1 TTGGTGTTGATCAATT
25292 TTGG
1 TTGG
25296 CAATTACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTGGTGTTGATCAATT
Found at i:25316 original size:4 final size:4
Alignment explanation
Indices: 25307--25398 Score: 125
Period size: 4 Copynumber: 23.5 Consensus size: 4
25297 AATTACCATG
25307 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T--A TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
25353 CACA AACA TACA TACA TACA TACA TATA TACA CACA AACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
25399 TATATATATA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.03
4 76 0.97
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (4 bp):
TACA
Found at i:25519 original size:22 final size:22
Alignment explanation
Indices: 25477--25520 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25467 TATTCATATG
* *
25477 AAATTATGATAATCTCCCTATT
1 AAATTATAATAATCTCACTATT
25499 AAATTATAATAAT-TACACTATT
1 AAATTATAATAATCT-CACTATT
25521 TTTTATGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATTATAATAATCTCACTATT
Found at i:25553 original size:22 final size:22
Alignment explanation
Indices: 25528--25573 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
25518 ATTTTTTATG
*
25528 ACCTCCTTATAAAATTTTAATA
1 ACCTCCATATAAAATTTTAATA
* *
25550 ACCTTCATATGAAATTTTAATA
1 ACCTCCATATAAAATTTTAATA
25572 AC
1 AC
25574 GATACTATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (22 bp):
ACCTCCATATAAAATTTTAATA
Found at i:25619 original size:22 final size:22
Alignment explanation
Indices: 25593--25641 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
25583 GAATTTCAAG
* *
25593 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
25615 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
25637 AACCT
1 AACCT
25642 CCCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:25715 original size:22 final size:22
Alignment explanation
Indices: 25623--26069 Score: 291
Period size: 22 Copynumber: 20.6 Consensus size: 22
25613 TTAACCTTCT
* *
25623 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
25645 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCAC
** *
25667 TATGAAATTTTGATAATTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
25689 AATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCAC
* *
25711 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
25732 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
25755 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
25776 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* *
25799 TCA-GAAATTTTGATAATCACAC
1 T-ATGAAATTTTGATAACCTCAC
* *
25821 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
25843 TATGAAATTTTGATAAGCCTCGC
1 TATGAAATTTTGATAA-CCTCAC
*
25866 TATAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
*
25887 TTATGAAATCTTGATAA-CT-AC
1 -TATGAAATTTTGATAACCTCAC
* *
25908 ----AAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
25926 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * * *
25948 TATAAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
*
25970 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
25992 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
26014 TATGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
26036 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
26057 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
26070 TACTCCATAA
Statistics
Matches: 332, Mismatches: 66, Indels: 56
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 14 0.04
21 15 0.05
22 252 0.76
23 36 0.11
24 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:25944 original size:105 final size:104
Alignment explanation
Indices: 25803--26010 Score: 265
Period size: 105 Copynumber: 2.0 Consensus size: 104
25793 TCACACTCAG
* * *
25803 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAGCCTCGCTA
1 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCACTATAAAATTTTGATAA-CCTCCCTA
*
25868 TAAAATTTTGATAA-CCTCCTTATGAAATCTTGATAACTAC
65 TAAAATTTTGATAACCCT-CTTATGAAATCTTGAAAACTAC
* * ** * * * *
25908 AAATTTTGATAATCTCCCTATGATTTTTTGATAACCTCATTATAAAATTTTGTTAATCTCCCTAT
1 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCACTATAAAATTTTGATAACCTCCCTAT
* *
25973 GAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTA
66 AAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTA
26011 AACTATGAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
104 38 0.43
105 50 0.57
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (104 bp):
AAATTTTGATAATCACACTATGAAATTGTGATAACCTCACTATAAAATTTTGATAACCTCCCTAT
AAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTAC
Found at i:25984 original size:82 final size:83
Alignment explanation
Indices: 25825--25986 Score: 218
Period size: 82 Copynumber: 2.0 Consensus size: 83
25815 TCACACTATG
* * *
25825 AAATTGTGATAACCTCGCTATGAAATTTTGATAAGCCTCGCTATAAAATTTTGATAACCTCCTTA
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAAGCCTCACTATAAAATTTTGATAACCTCCCTA
25890 TGAAATCTTGATAACTAC
66 TGAAATCTTGATAACTAC
* * ** * * *
25908 AAATTTTGATAATCTCCCTATGATTTTTTGATAA-CCTCATTATAAAATTTTGTTAATCTCCCTA
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAAGCCTCACTATAAAATTTTGATAACCTCCCTA
*
25972 TGAAATTTTGATAAC
66 TGAAATCTTGATAAC
25987 CCTCTTATGA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
82 39 0.57
83 29 0.43
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (83 bp):
AAATTGTGATAACCTCCCTATGAAATTTTGATAAGCCTCACTATAAAATTTTGATAACCTCCCTA
TGAAATCTTGATAACTAC
Found at i:26209 original size:22 final size:22
Alignment explanation
Indices: 26177--26591 Score: 197
Period size: 22 Copynumber: 18.6 Consensus size: 22
26167 TCACATTTTG
*
26177 GAAA-TTTGATAACCTCTTTAT
1 GAAATTTTGATAACCTCTCTAT
26198 GAAATTTTGATAACCTCTCTAT
1 GAAATTTTGATAACCTCTCTAT
* * * *
26220 AAAATTTTGTTGACCCCTCTAT
1 GAAATTTTGATAACCTCTCTAT
* ***
26242 AAAATTTTGATATTTTCAT-TAT
1 GAAATTTTGATAACCTC-TCTAT
* * *
26264 GTAATTTTGATAACCTCGCTTT
1 GAAATTTTGATAACCTCTCTAT
** *
26286 GAAATTTTGATAACAACACTAT
1 GAAATTTTGATAACCTCTCTAT
* *
26308 GGAATTTTGATAATCT-TCCTAT
1 GAAATTTTGATAACCTCT-CTAT
26330 -AAATTTTGATAATCCGATCTCTAT
1 GAAATTTTGATAA-CC--TCTCTAT
* * * *
26354 AAAATTTCGATAATCACTCTAT
1 GAAATTTTGATAACCTCTCTAT
*
26376 GAGA-TTTGATAACCT-TCTAT
1 GAAATTTTGATAACCTCTCTAT
* ** * *
26396 CAAATTTTGGCACTCCT-TATAAAATT
1 GAAATTTTGATA-ACCTCTCT---A-T
*
26422 GAGACTTTT-ATAACCT-TCATAT
1 GA-AATTTTGATAACCTCTC-TAT
* * * *
26444 GAAATTTTGGTAACCACACTAA
1 GAAATTTTGATAACCTCTCTAT
* * * *
26466 AAAATTTTAATAACCACACTAT
1 GAAATTTTGATAACCTCTCTAT
* *
26488 GAAATTTTTGGTAACCTCCCTAT
1 GAAA-TTTTGATAACCTCTCTAT
*
26511 GAAATATT-AGTAACCTC-CTTAT
1 GAAATTTTGA-TAACCTCTC-TAT
* *
26533 GAAATTTTGGTAACCATATACTAT
1 GAAATTTTGATAACC-TCT-CTAT
*
26557 GAAATTCTT-ATAACCTCGCTAT
1 GAAATT-TTGATAACCTCTCTAT
*
26579 GACATTTTGATAA
1 GAAATTTTGATAA
26592 TATCTTTGAT
Statistics
Matches: 293, Mismatches: 73, Indels: 55
0.70 0.17 0.13
Matches are distributed among these distances:
20 7 0.02
21 36 0.12
22 178 0.61
23 23 0.08
24 20 0.07
25 20 0.07
26 4 0.01
27 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTCTAT
Found at i:26525 original size:45 final size:44
Alignment explanation
Indices: 26441--26548 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 44
26431 ATAACCTTCA
*
26441 TATGAAATTTTGGTAACCACACTAAAAAATTTTAATAACCACAC-
1 TATGAAATTTTGGTAACCACACTAAAAAATATTAATAACCAC-CT
* * ** * *
26485 TATGAAATTTTTGGTAACCTCCCTATGAAATATTAGTAACCTCCT
1 TATGAAA-TTTTGGTAACCACACTAAAAAATATTAATAACCACCT
26530 TATGAAATTTTGGTAACCA
1 TATGAAATTTTGGTAACCA
26549 TATACTATGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 19 0.35
45 35 0.65
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCACACTAAAAAATATTAATAACCACCT
Found at i:26708 original size:22 final size:22
Alignment explanation
Indices: 26596--26807 Score: 162
Period size: 22 Copynumber: 9.5 Consensus size: 22
26586 TGATAATATC
** *
26596 TTTGATAACCTTTTTATAAAAT
1 TTTGATAACCTTCCTATGAAAT
* *
26618 TGTGATAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
** **
26640 TTCAATAACCTTCCTAAAAAATT
1 TTTGATAACCTTCCTATGAAA-T
*
26663 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
*
26687 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
26709 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCTTCC-TATGAAAT
* * *
26731 TTTGGTAACC-ACACTATGGAAT
1 TTTGATAACCTTC-CTATGAAAT
26753 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * * *
26775 TATAATAAACCATCTTATGAAAT
1 TTTGAT-AACCTTCCTATGAAAT
26798 TTTGATAACC
1 TTTGATAACC
26808 ACACAGAGAC
Statistics
Matches: 151, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
21 7 0.05
22 93 0.62
23 29 0.19
24 14 0.09
25 8 0.05
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:26709 original size:47 final size:43
Alignment explanation
Indices: 26631--26740 Score: 112
Period size: 47 Copynumber: 2.4 Consensus size: 43
26621 GATAACCACA
** *
26631 CTATGAAATTTCAATAACCTTCCTAAAAAATTTTTAATAACCTGATC
1 CTATGAAATTTTGATAACCTTCCCAAAAAA-TTTTAATAA-CT--TC
** *
26678 CTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTC
1 CTATGAAATTTTGATAACCTTCCCAAAAAATTTTAATAACTTC
*
26721 CATATGAAATTTTGGTAACC
1 C-TATGAAATTTTGATAACC
26741 ACACTATGGA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
43 3 0.05
44 17 0.31
45 2 0.04
46 8 0.15
47 25 0.45
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.37
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTTCCCAAAAAATTTTAATAACTTC
Found at i:27306 original size:13 final size:13
Alignment explanation
Indices: 27270--27308 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
27260 TGTAAATTGA
27270 AATTTT-ATAATT
1 AATTTTAATAATT
27282 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
27297 AATTTTAATAAT
1 AATTTTAATAAT
27309 GTCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 4 0.17
15 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:27316 original size:15 final size:14
Alignment explanation
Indices: 27276--27308 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
27266 TTGAAATTTT
27276 ATAATTAATTTTTAA
1 ATAATTAA-TTTTAA
27291 ATAATTAATTTT-A
1 ATAATTAATTTTAA
27304 ATAAT
1 ATAAT
27309 GTCAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTAATTTTAA
Found at i:30913 original size:25 final size:24
Alignment explanation
Indices: 30866--30913 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
30856 AGTTTATCAC
*
30866 AATTTCATAGGTAATTATTAAAAA
1 AATTTCATAGGTAATTATCAAAAA
* *
30890 AATTTCGTAGGTTGATTATCAAAA
1 AATTTCATAGG-TAATTATCAAAA
30914 TTTAATAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (24 bp):
AATTTCATAGGTAATTATCAAAAA
Found at i:45175 original size:28 final size:27
Alignment explanation
Indices: 45133--45187 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
45123 TTTTTATTTG
*
45133 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
45159 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
45188 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:50317 original size:66 final size:66
Alignment explanation
Indices: 50241--50373 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
50231 CACTGGACCA
50241 GCAGCTTGGCATATCTGCAATCCATGGCATGTATGATGTAAGCAAAAACAAGAAAATCCCATGGA
1 GCAGCTTGGCATATCTGCAATCCATGGCATGTATGATGTAAGCAAAAACAAGAAAATCCCATGGA
50306 C
66 C
*
50307 GCAGCTTGGCATATCTGCAATCCATGGCATGTATGATGTAAGCAAAAACAAGAAAATTCCATGGA
1 GCAGCTTGGCATATCTGCAATCCATGGCATGTATGATGTAAGCAAAAACAAGAAAATCCCATGGA
50372 C
66 C
50373 G
1 G
50374 TTCAAACATG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (66 bp):
GCAGCTTGGCATATCTGCAATCCATGGCATGTATGATGTAAGCAAAAACAAGAAAATCCCATGGA
C
Found at i:53611 original size:2 final size:2
Alignment explanation
Indices: 53606--53639 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53596 CAGGGTTTAA
53606 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
53640 ACCAAACCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54386 original size:6 final size:6
Alignment explanation
Indices: 54370--54404 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
54360 CAAACAGATA
*
54370 GTATAT ATATAT GTATAT GTATAT GTA-AT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
54405 ATTTAAGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (6 bp):
GTATAT
Found at i:55683 original size:23 final size:23
Alignment explanation
Indices: 55653--55700 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
55643 AATTGATGTC
*
55653 CATTAACATTAATATATGACTTT
1 CATTAACATTAATACATGACTTT
55676 CATTAACATTAATACATGACTTT
1 CATTAACATTAATACATGACTTT
55699 CA
1 CA
55701 ACAAATCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (23 bp):
CATTAACATTAATACATGACTTT
Found at i:57656 original size:60 final size:61
Alignment explanation
Indices: 57574--57731 Score: 187
Period size: 60 Copynumber: 2.6 Consensus size: 61
57564 AATTGCTCAT
* * * *
57574 ATAA-GGATCTAATGTTTATCAAAATGCTCAAATAAGGGTCT-GATCTTTTAATTTGGCCAA
1 ATAAGGGA-CTAATGTTTGTCAAAATGCTCAAATAAGGGACTCGATATTTTAATTTAGCCAA
* * * *
57634 ATGAGGGACTAATATTTGTCAAAATGTTCAAATAA-GGACTCGATATTTTAATTTAGCTAA
1 ATAAGGGACTAATGTTTGTCAAAATGCTCAAATAAGGGACTCGATATTTTAATTTAGCCAA
* * *
57694 ATAAGGGCCTAATGTATGCCAAAATGCTCAAATAAGGG
1 ATAAGGGACTAATGTTTGTCAAAATGCTCAAATAAGGG
57732 CCTGGCGTCG
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 4 0.05
60 72 0.89
61 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (61 bp):
ATAAGGGACTAATGTTTGTCAAAATGCTCAAATAAGGGACTCGATATTTTAATTTAGCCAA
Found at i:57868 original size:29 final size:30
Alignment explanation
Indices: 57804--57919 Score: 123
Period size: 29 Copynumber: 3.9 Consensus size: 30
57794 CGATAACGTT
57804 AGGCCCTTATTTGGCCAAATTAAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAAGATC
*
57834 AGGCCCTTATTTGGTCAAATT-AAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAAGATC
* * * *
57863 ATGCCCTTATTTGACC-AGTTGCGATAACA-AT-
1 AGGCCCTTATTTGGCCAAATT---A-AAAAGATC
57894 AGGCCCTTATTTGGCCAAATTAAAAA
1 AGGCCCTTATTTGGCCAAATTAAAAA
57920 ATTGGGCTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.09
29 22 0.31
30 20 0.29
31 14 0.20
32 5 0.07
33 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (30 bp):
AGGCCCTTATTTGGCCAAATTAAAAAGATC
Found at i:63182 original size:34 final size:34
Alignment explanation
Indices: 63116--63182 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
63106 ATCAAGTACC
* * *
63116 AAGTAATCATTCTATATATATATATTTCTTGAAA
1 AAGTAACCATTCTATATATACATATTACTTGAAA
63150 AAGTAACCATTCTATATATACATA-TACATTGAA
1 AAGTAACCATTCTATATATACATATTAC-TTGAA
63183 CAGATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (34 bp):
AAGTAACCATTCTATATATACATATTACTTGAAA
Found at i:64161 original size:2 final size:2
Alignment explanation
Indices: 64154--64192 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
64144 ACAATGGTGT
64154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64193 TTCTGGTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.