Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024672.1 Corchorus olitorius cultivar O-4 contig24705, 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: 27281
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:10177 original size:19 final size:18
Alignment explanation
Indices: 10152--10188 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
10142 AGGGTAATTT
*
10152 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAATGTTTTCA
10170 TAAAAAAAAATGTTTTCA
1 TAAAAAAAAATGTTTTCA
10188 T
1 T
10189 GATAGAGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAATGTTTTCA
Found at i:11501 original size:96 final size:96
Alignment explanation
Indices: 11334--11625 Score: 410
Period size: 96 Copynumber: 3.0 Consensus size: 96
11324 AAAACATGAA
* * * * **
11334 TGAAATCAACACCTTCCGATGGGGAAAGGCAAAACGGGAATAAAACT-TTCGAAACAACACCTTC
1 TGAAAACAACACCTTCCGATCGGGAAGGGCAAAACAGGAATAAAA-TATTAAAAACAACACCTTC
** *
11398 CGACCGGGAAGGGCAAAACAAGAATAAAACAT
65 CGACCGGGAAGGGCAAAACGGGAATAAAATAT
* *
11430 TGAAACCAACACCTTCCGATCGGGAAGGGCAAAACAGGAATATAATATTAAAAACAACACCTTCC
1 TGAAAACAACACCTTCCGATCGGGAAGGGCAAAACAGGAATAAAATATTAAAAACAACACCTTCC
*
11495 -AGCCGGGAAGGGCAAAACGGGAATAAAATAC
66 GA-CCGGGAAGGGCAAAACGGGAATAAAATAT
* *
11526 TGAAAACGACACCTTCCGATCGGGAAGGGCAAAA-AGGGAATAAAATACTAAAAACAACACCTTC
1 TGAAAACAACACCTTCCGATCGGGAAGGGCAAAACA-GGAATAAAATATTAAAAACAACACCTTC
11590 CGACCGGGAAGGGCAAAACGGGAATAAAATAT
65 CGACCGGGAAGGGCAAAACGGGAATAAAATAT
11622 TGAA
1 TGAA
11626 GGAAAACTGG
Statistics
Matches: 176, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
95 3 0.02
96 172 0.98
97 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (96 bp):
TGAAAACAACACCTTCCGATCGGGAAGGGCAAAACAGGAATAAAATATTAAAAACAACACCTTCC
GACCGGGAAGGGCAAAACGGGAATAAAATAT
Found at i:11620 original size:48 final size:48
Alignment explanation
Indices: 11340--11622 Score: 363
Period size: 48 Copynumber: 5.9 Consensus size: 48
11330 TGAATGAAAT
** * **
11340 CAACACCTTCCGATGGGGAAAGGCAAAACGGGAATAAAACT-TTCGAAA
1 CAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAA-TATTAAAAA
** * * *
11388 CAACACCTTCCGACCGGGAAGGGCAAAACAAGAATAAAACATTGAAAC
1 CAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATTAAAAA
* * *
11436 CAACACCTTCCGATCGGGAAGGGCAAAACAGGAATATAATATTAAAAA
1 CAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATTAAAAA
* *
11484 CAACACCTTCC-AGCCGGGAAGGGCAAAACGGGAATAAAATACTGAAAA
1 CAACACCTTCCGA-CCGGGAAGGGCAAAACGGGAATAAAATATTAAAAA
* * * *
11532 CGACACCTTCCGATCGGGAAGGGCAAAAAGGGAATAAAATACTAAAAA
1 CAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATTAAAAA
11580 CAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATT
1 CAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATT
11623 GAAGGAAAAC
Statistics
Matches: 204, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
47 1 0.00
48 202 0.99
49 1 0.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (48 bp):
CAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATTAAAAA
Found at i:11655 original size:53 final size:48
Alignment explanation
Indices: 11344--11655 Score: 216
Period size: 48 Copynumber: 6.4 Consensus size: 48
11334 TGAAATCAAC
* * * *
11344 ACCTTCCGA-TGGGGAAAGGCAAAACGGGAATAAAACTTTCGAA-ACAAC-
1 ACCTTCCGACT-GGGAAGGGCAAAACGGGAATAAAA--TACTAAGAAAACG
* ** * * *
11392 ACCTTCCGACCGGGAAGGGCAAAACAAGAATAAAACATTGAA-ACCAAC-
1 ACCTTCCGACTGGGAAGGGCAAAACGGGAATAAAATACT-AAGA-AAACG
* * * *
11440 ACCTTCCGA-TCGGGAAGGGCAAAACAGGAATATAATATTAAAAACAAC-
1 ACCTTCCGACT-GGGAAGGGCAAAACGGGAATAAAATACTAAGAA-AACG
*
11488 ACCTTCC-AGCCGGGAAGGGCAAAACGGGAATAAAATACT--GAAAACG
1 ACCTTCCGA-CTGGGAAGGGCAAAACGGGAATAAAATACTAAGAAAACG
* *
11534 ACACCTTCCGA-TCGGGAAGGGCAAAAAGGGAATAAAATACTAAAAACAAC-
1 --ACCTTCCGACT-GGGAAGGGCAAAACGGGAATAAAATACTAAGAA-AACG
* *
11584 ACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATATTGAAGGAAAACTGGG
1 ACCTTCCGACTGGGAAGGGCAAAACGGGAATAAAATACT-AA-GAAAAC---G
11637 ACCTTCCGACTGGGAAGGG
1 ACCTTCCGACTGGGAAGGG
11656 TCATTTTTGC
Statistics
Matches: 215, Mismatches: 26, Indels: 41
0.76 0.09 0.15
Matches are distributed among these distances:
45 3 0.01
46 2 0.01
47 6 0.03
48 173 0.80
49 6 0.03
50 4 0.02
51 3 0.01
53 18 0.08
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (48 bp):
ACCTTCCGACTGGGAAGGGCAAAACGGGAATAAAATACTAAGAAAACG
Found at i:11811 original size:86 final size:86
Alignment explanation
Indices: 11627--12166 Score: 469
Period size: 86 Copynumber: 6.0 Consensus size: 86
11617 AATATTGAAG
* * ** * * * * * *
11627 GAAAACTGGGACCTTCCGACTGGGAAGGGTCATTTTTGCAAATGAAAACAAGGACCTTCCGACTG
1 GAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTTG-AAAAGACAATAAAGACCTTCCGACCG
*
11692 GGAAGGGGCATTTTTGGAAA-T
65 GGAAGGGGCATTTTTGGAAAGA
* * *
11713 GAAAATAGGGACCTTCCAACCAGGAAGGGGCATTTTTGAAAAGACAATAAAGACCTTCCAACCAG
1 GAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTTGAAAAGACAATAAAGACCTTCCGACCGG
11778 GAAGGGGCATTTTTGGAAAGA
66 GAAGGGGCATTTTTGGAAAGA
* * * * * *
11799 GAATACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAGAGAATAAAGACCTTCCAACCAG
1 GAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTTGAAAAGACAATAAAGACCTTCCGACCGG
*
11864 GAAGGGGCATTTCTTGAAAGAGA
66 GAAGGGGCATTT-TTGGAA-AGA
* * * * *
11887 GAAAACTGTGACCTTCCGA-CAGGAAAGGGGCATTTTTGGAAAGAGACATTGAAAAGTGGGATCT
1 GAAAACAGGGACCTTCCAACCAGG-AAGGGGCATTTTT-GAAA-AGACAAT--AAA----GACCT
11951 TCCGACCGGGAAGGGGCATTTTTGGTATACA-A
57 TCCGACCGGGAAGGGGCATTTTTGG-A-A-AGA
* * * *
11983 GAAAATAGGGACCGTCCAACCAGGAA-GGGCATTTTTGGAAAGAGAGAA-AACTGTGACCTTCCG
1 GAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTT-GAAA-AGACAATAA---AGACCTTCCG
12046 ACCGGGAAGGGGCATTTTTGGAAATGAA
61 ACCGGGAAGGGGCATTTTTGGAAA-G-A
* * * * * *
12074 GAAAACTGGGACCTTCCGACCAGGAAGGGACATTTTTGAAGAGATATTGAAAACTAGGACCTTCC
1 GAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTTGAAAAGACA---ATAA--A-GACCTTCC
12139 GACCGGGAAGGGGCATTTTTGGAAAGA
60 GACCGGGAAGGGGCATTTTTGGAAAGA
12166 G
1 G
12167 GGAAAACAAT
Statistics
Matches: 375, Mismatches: 52, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
85 39 0.10
86 104 0.28
87 9 0.02
88 31 0.08
89 4 0.01
90 10 0.03
91 55 0.15
92 16 0.04
93 2 0.01
94 35 0.09
95 23 0.06
96 41 0.11
97 6 0.02
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (86 bp):
GAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTTGAAAAGACAATAAAGACCTTCCGACCGG
GAAGGGGCATTTTTGGAAAGA
Found at i:11917 original size:46 final size:46
Alignment explanation
Indices: 11627--12173 Score: 471
Period size: 46 Copynumber: 12.1 Consensus size: 46
11617 AATATTGAAG
** * * *
11627 GAAAACTGGGACCTTCCGACTGGGAAGGGTCATTTTT-GCAA-A-T
1 GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
** ** *
11670 GAAAACAAGGACCTTCCGACTGGGAAGGGGCATTTTTGG-AA-A-T
1 GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
*
11713 GAAAA-TAGGGACCTTCCAACCAGGAAGGGGCATTTTT-GAAA-AGA
1 GAAAACT-GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
* * *
11757 CAATAA---AGACCTTCCAACCAGGAAGGGGCATTTTTGG-AA-AGA
1 GAA-AACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
* ** *
11799 GAATACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAGAGA
1 GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
*
11845 -ATAAA----GACCTTCCAACCAGGAAGGGGCATTTCTT-GAAAGAGA
1 GA-AAACTGGGACCTTCCGACCAGGAAGGGGCATTT-TTGGAAAGAGA
*
11887 GAAAACTGTGACCTTCCGA-CAGGAAAGGGGCATTTTTGGAAAGAGACA
1 GAAAACTGGGACCTTCCGACCAGG-AAGGGGCATTTTTGGAAAGAG--A
* * * * *
11935 TTGAAAAGTGGGATCTTCCGACCGGGAAGGGGCATTTTTGGTATACA-A
1 --GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGG-AAAGAGA
* *
11983 GAAAA-TAGGGACCGTCCAACCAGGAA-GGGCATTTTTGGAAAGAGA
1 GAAAACT-GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
* *
12028 GAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATGA-A
1 GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAA-GAGA
* *
12074 GAAAACTGGGACCTTCCGACCAGGAAGGGACATTTTT-GAAGAGATA
1 GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAA-AGAGA
* * *
12120 TTGAAAACTAGGACCTTCCGACCGGGAAGGGGCATTTTTGGAAAGAGG
1 --GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
12168 GAAAAC
1 GAAAAC
12174 AATTTTCGGT
Statistics
Matches: 428, Mismatches: 40, Indels: 69
0.80 0.07 0.13
Matches are distributed among these distances:
41 1 0.00
42 73 0.17
43 76 0.18
44 36 0.08
45 50 0.12
46 111 0.26
47 2 0.00
48 39 0.09
49 3 0.01
50 31 0.07
51 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (46 bp):
GAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAAGAGA
Found at i:12909 original size:50 final size:50
Alignment explanation
Indices: 12745--13091 Score: 230
Period size: 50 Copynumber: 6.9 Consensus size: 50
12735 CAAAAATTTC
* * * * *
12745 ATCTTTATTTACAAATTAGTTAACAG-TTCAATATTTTAACTTAAAGATTTC-
1 ATCTTTATTTACAAATTACTTAAAAGTTTCAA-CTTTTAA-TTAAA-AATCCA
* ** * *
12796 ATTTTTATTTACAAATTGTTTAAAAGGTTTCAACTTTTCATTAAAAATCCC
1 ATCTTTATTTACAAATTACTTAAAA-GTTTCAACTTTTAATTAAAAATCCA
** * * *
12847 ATCTTTGCTTACAAATTACTTAAAAGTTTGATCTTTTAATCTAGAAA-CCA
1 ATCTTTATTTACAAATTACTTAAAAGTTTCAACTTTTAAT-TAAAAATCCA
* * * * *
12897 ATCTTTATTTACAAACTACTTAAAAGCTTCAATCCTTTAGTT-AAAGTCCA
1 ATCTTTATTTACAAATTACTTAAAAGTTTCAA-CTTTTAATTAAAAATCCA
* * * * * * *
12947 ACCTCTATTTACCATTTTCTTAAAAG-TTCAATCTTTTATTTAAAAGTCCA
1 ATCTTTATTTACAAATTACTTAAAAGTTTCAA-CTTTTAATTAAAAATCCA
* *
12997 A-CTTTTATTTACAAAATT-CTTAAAAG-TTCAATCTTTTAATTAAAAGTTCA
1 ATC-TTTATTTAC-AAATTACTTAAAAGTTTCAA-CTTTTAATTAAAAATCCA
*
13047 TATTTTTA-TTACAAAATT-CTTAAAAG-TTCAATCTTTTAATTAAAA
1 -ATCTTTATTTAC-AAATTACTTAAAAGTTTCAA-CTTTTAATTAAAA
13092 GTTCATATTT
Statistics
Matches: 243, Mismatches: 42, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
49 16 0.07
50 151 0.62
51 65 0.27
52 6 0.02
53 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (50 bp):
ATCTTTATTTACAAATTACTTAAAAGTTTCAACTTTTAATTAAAAATCCA
Found at i:13001 original size:19 final size:20
Alignment explanation
Indices: 12966--13007 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12956 TACCATTTTC
*
12966 TTAAAAGTTCAATCTTTTAT
1 TTAAAAGTCCAATCTTTTAT
12986 TTAAAAGTCCAA-CTTTTAT
1 TTAAAAGTCCAATCTTTTAT
13005 TTA
1 TTA
13008 CAAAATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (20 bp):
TTAAAAGTCCAATCTTTTAT
Found at i:13004 original size:100 final size:100
Alignment explanation
Indices: 12855--13093 Score: 256
Period size: 100 Copynumber: 2.4 Consensus size: 100
12845 CCATCTTTGC
** *
12855 TTAC-AAATTACTTAAAAGTTTGATCTTTTAATCTAGAAA--CCAA-TCTTTATTTACAAACTAC
1 TTACAAAATT-CTTAAAAGTTCAATCTTTTAAT-TA-AAAGTCCAACT-TTTATTTACAAAATAC
*
12916 TTAAAAGCTTCAATCCTTTAGTT-AAAGTCCA-ACCTCTA
62 TTAAAAG-TTCAATCCTTTAATTAAAAGTCCATACCTCTA
* ** * *
12954 TTTACCATTTTCTTAAAAGTTCAATCTTTTATTTAAAAGTCCAACTTTTATTTACAAAATTCTTA
1 -TTACAAAATTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAACTTTTATTTACAAAATACTTA
* * ** *
13019 AAAGTTCAATCTTTTAATTAAAAGTTCATATTTTTA
65 AAAGTTCAATCCTTTAATTAAAAGTCCATACCTCTA
13055 TTACAAAATTCTTAAAAGTTCAATCTTTTAATTAAAAGT
1 TTACAAAATTCTTAAAAGTTCAATCTTTTAATTAAAAGT
13094 TCATATTTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
98 3 0.03
99 15 0.13
100 90 0.78
101 8 0.07
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (100 bp):
TTACAAAATTCTTAAAAGTTCAATCTTTTAATTAAAAGTCCAACTTTTATTTACAAAATACTTAA
AAGTTCAATCCTTTAATTAAAAGTCCATACCTCTA
Found at i:13092 original size:50 final size:50
Alignment explanation
Indices: 12963--13109 Score: 251
Period size: 50 Copynumber: 2.9 Consensus size: 50
12953 ATTTACCATT
* * *
12963 TTCTTAAAAGTTCAATCTTTTATTTAAAAGTCCA-ACTTTTATTTACAAAA
1 TTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCATATTTTTA-TTACAAAA
13013 TTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCATATTTTTATTACAAAA
1 TTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCATATTTTTATTACAAAA
13063 TTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCATATTTTTATTACA
1 TTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCATATTTTTATTACA
13110 CAACACTCAT
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
50 87 0.94
51 6 0.06
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (50 bp):
TTCTTAAAAGTTCAATCTTTTAATTAAAAGTTCATATTTTTATTACAAAA
Found at i:13104 original size:20 final size:20
Alignment explanation
Indices: 13016--13096 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
13006 TACAAAATTC
13016 TTAAAAGTTCAATCTTTTAA
1 TTAAAAGTTCAATCTTTTAA
*
13036 TTAAAAGTTCATATTTTTATTACAAAA
1 TTAAAAGTTCA-A-TCTT-TT----AA
13063 TTCTTAAAAGTTCAATCTTTTAA
1 ---TTAAAAGTTCAATCTTTTAA
13086 TTAAAAGTTCA
1 TTAAAAGTTCA
13097 TATTTTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 20
0.69 0.03 0.28
Matches are distributed among these distances:
20 22 0.45
21 1 0.02
22 3 0.06
23 4 0.08
27 4 0.08
28 3 0.06
29 1 0.02
30 11 0.22
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
TTAAAAGTTCAATCTTTTAA
Found at i:19724 original size:30 final size:30
Alignment explanation
Indices: 19688--19766 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 30
19678 ATTTTATTAA
* *
19688 TTTCCAAAATCTTCTTT-CATATTTCTTTAT
1 TTTCCAAAATCTTCTTTGCA-ATTACCTTAT
*
19718 TTTCCAAAATCTTCTTTTGGGAATTACCTTAT
1 TTTCCAAAATCTTC-TTT-GCAATTACCTTAT
19750 TTTCCAAAATCTTCTTT
1 TTTCCAAAATCTTCTTT
19767 TGGACTTGCT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.33
31 6 0.14
32 22 0.51
33 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (30 bp):
TTTCCAAAATCTTCTTTGCAATTACCTTAT
Found at i:22572 original size:27 final size:27
Alignment explanation
Indices: 22541--22592 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
22531 AGAAGATTTT
22541 TGAAGAGGGAGAGGGGCGATGAGAGTG
1 TGAAGAGGGAGAGGGGCGATGAGAGTG
*
22568 TGAAGAGTGAGAGGGGCGATGAGAG
1 TGAAGAGGGAGAGGGGCGATGAGAG
22593 AGATTGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.54, T:0.12
Consensus pattern (27 bp):
TGAAGAGGGAGAGGGGCGATGAGAGTG
Found at i:23940 original size:11 final size:11
Alignment explanation
Indices: 23920--23949 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
23910 TGCAAAGTTA
*
23920 CTTTTCTTTTT
1 CTTTTTTTTTT
23931 CTTTTTTTTTT
1 CTTTTTTTTTT
23942 CTTTTTTT
1 CTTTTTTT
23950 GCTCATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:24269 original size:26 final size:26
Alignment explanation
Indices: 24240--24294 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
24230 ATTAATCAAT
*
24240 ATGCAATGCAAGATATGATATACTAA
1 ATGCAATGCAAGATATGACATACTAA
* *
24266 ATGCAATGTAAGATATGACATGCTAA
1 ATGCAATGCAAGATATGACATACTAA
24292 ATG
1 ATG
24295 TAACATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (26 bp):
ATGCAATGCAAGATATGACATACTAA
Found at i:27243 original size:2 final size:2
Alignment explanation
Indices: 27238--27281 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
27228 TGCTTTCCTT
27238 TA TA TA TA TA TA 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 TA TA TA TA TA TA
27280 TA
1 TA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.