Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014200.1 Corchorus olitorius cultivar O-4 contig14233, 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: 61003
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5117 original size:22 final size:22
Alignment explanation
Indices: 5092--5158 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
5082 GCTAGGCCGG
*
5092 CCATGGTCTGGCTACCCGCGCA
1 CCATGGCCTGGCTACCCGCGCA
5114 CCATGGCCTGGCTACCCGCGCA
1 CCATGGCCTGGCTACCCGCGCA
*
5136 CCATGGCCTGTCTACCCGCGCA
1 CCATGGCCTGGCTACCCGCGCA
5158 C
1 C
5159 TATACCCAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.13, C:0.45, G:0.25, T:0.16
Consensus pattern (22 bp):
CCATGGCCTGGCTACCCGCGCA
Found at i:7155 original size:43 final size:43
Alignment explanation
Indices: 7108--7194 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
7098 AAGTTCGTGA
7108 TTGAAGATAATTTGAAGATTTGAAGACTATTGAAGAACATCTC
1 TTGAAGATAATTTGAAGATTTGAAGACTATTGAAGAACATCTC
7151 TTGAAGATAATTTGAAGATTTGAAGACTATTGAAGAACATCTC
1 TTGAAGATAATTTGAAGATTTGAAGACTATTGAAGAACATCTC
7194 T
1 T
7195 AGAGAAAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (43 bp):
TTGAAGATAATTTGAAGATTTGAAGACTATTGAAGAACATCTC
Found at i:7209 original size:43 final size:43
Alignment explanation
Indices: 7110--7213 Score: 147
Period size: 43 Copynumber: 2.4 Consensus size: 43
7100 GTTCGTGATT
* * *
7110 GAAGATAATTTGAAGATTTGAAGACTATTGAAGAACATCTCTT
1 GAAGAAAAATTGAAGATTTGAAGACTATTGAAGAACATCTCTA
* *
7153 GAAGATAATTTGAAGATTTGAAGACTATTGAAGAACATCTCTA
1 GAAGAAAAATTGAAGATTTGAAGACTATTGAAGAACATCTCTA
7196 G-AGAAAGAATTGAAGATT
1 GAAGAAA-AATTGAAGATT
7214 GGAGCTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 4 0.07
43 53 0.93
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (43 bp):
GAAGAAAAATTGAAGATTTGAAGACTATTGAAGAACATCTCTA
Found at i:9460 original size:32 final size:32
Alignment explanation
Indices: 9388--9469 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
9378 ATTTTACTAA
** *
9388 TTTCCAAAATCTCCTTTT-GAATTTCCTTATT
1 TTTCCAAAATCTCCTTTTGGAATAACCTTATC
*
9419 TTTCCAAAATCTCCTTTTGGGGATAACCTTA-C
1 TTTCCAAAATCTCCTTTT-GGAATAACCTTATC
*
9451 TTTCCAAAATCTTCTTTTG
1 TTTCCAAAATCTCCTTTTG
9470 AAGTTTACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 19 0.43
32 17 0.39
33 8 0.18
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.46
Consensus pattern (32 bp):
TTTCCAAAATCTCCTTTTGGAATAACCTTATC
Found at i:17197 original size:4 final size:4
Alignment explanation
Indices: 17190--17286 Score: 194
Period size: 4 Copynumber: 24.2 Consensus size: 4
17180 CATATATATC
17190 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
17238 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
17286 T
1 T
17287 ATATATATAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 93 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:17291 original size:4 final size:4
Alignment explanation
Indices: 17284--17315 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
17274 TGTATGTATG
17284 TATA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA
17316 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:17295 original size:6 final size:6
Alignment explanation
Indices: 17284--17315 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
17274 TGTATGTATG
17284 TATATA TATATA TATATA TATATA TATATA TA
1 TATATA TATATA TATATA TATATA TATATA TA
17316 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:17320 original size:2 final size:2
Alignment explanation
Indices: 17315--17384 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
17305 ATATATATAT
17315 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17357 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17385 TGAAAATTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17494 original size:29 final size:31
Alignment explanation
Indices: 17461--17519 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
17451 ATGAAAGATA
17461 AATTA-TTT-TAAGAAGCTAAAAAGAAAAAG
1 AATTATTTTATAAGAAGCTAAAAAGAAAAAG
* *
17490 AATTATTTTATAAGGAGTTAAAAAGAAAAA
1 AATTATTTTATAAGAAGCTAAAAAGAAAAA
17520 AGTTCAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 3 0.12
31 18 0.69
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.27
Consensus pattern (31 bp):
AATTATTTTATAAGAAGCTAAAAAGAAAAAG
Found at i:17922 original size:13 final size:13
Alignment explanation
Indices: 17900--17939 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
17890 CAGAGAATAT
17900 TATCAACAGAAGA
1 TATCAACAGAAGA
*
17913 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
17926 TTTCAACTGAAGA
1 TATCAACAGAAGA
17939 T
1 T
17940 TATTTGGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:18277 original size:15 final size:16
Alignment explanation
Indices: 18254--18286 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
18244 TGATCTTCCA
*
18254 ATCTTAAGTT-TTTAT
1 ATCTAAAGTTGTTTAT
18269 ATCTAAAGTTGTTTAT
1 ATCTAAAGTTGTTTAT
18285 AT
1 AT
18287 TGTTATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (16 bp):
ATCTAAAGTTGTTTAT
Found at i:20731 original size:19 final size:20
Alignment explanation
Indices: 20690--20731 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
20680 ATTTTCAAGT
* *
20690 AAAAATCTAAACTTTAGATC
1 AAAAATCCAAACTTTAGAAC
*
20710 AAAAATCCAACCTTTA-AAC
1 AAAAATCCAAACTTTAGAAC
20729 AAA
1 AAA
20732 TCCTAACTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAATCCAAACTTTAGAAC
Found at i:22916 original size:17 final size:17
Alignment explanation
Indices: 22894--22927 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22884 AAATGAAAAT
*
22894 ATTTTTGTGATTTTATG
1 ATTTTTCTGATTTTATG
*
22911 ATTTTTCTGTTTTTATG
1 ATTTTTCTGATTTTATG
22928 TGCCTTTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.68
Consensus pattern (17 bp):
ATTTTTCTGATTTTATG
Found at i:23794 original size:35 final size:34
Alignment explanation
Indices: 23682--24742 Score: 956
Period size: 35 Copynumber: 30.3 Consensus size: 34
23672 GAGTAAAATC
* *
23682 GAAGAAAGACCACTCTGGGTCAAATGAAAT--ACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
* * * *
23715 GAAGAACGACCACCCTCGATCATTCTGACATAAACT
1 GAAGAAAGACCACCCT-GGTCA-ACTGAAATAAACT
*
23751 GAAGAAAGACCACCCTAGGTCAACTGAAATAAATT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
* * *
23786 GAAAAAAGACCACCTTGGGTCAACTGAAATAAATT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
*
23821 GAAGAAAGACCACCCTGGGTCAATTGAAATAAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
*
23856 GAAGAAAGACCACCCTAGGTCAACAGAAATAAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
* * *
23891 GAAGAAAGACCGCCCTGGATTAA-TCGAAATAGACT
1 GAAGAAAGACCACCCTGG-TCAACT-GAAATAAACT
*
23926 GAAGAAAGA-CAGCCTGGGTCAACTGAAATAAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
* * * * * *
23960 AAATAAAGATCGCCCTGGATCAATTGAAATTAACT
1 GAAGAAAGACCACCCTGG-TCAACTGAAATAAACT
* * *
23995 AAAGAAAGATCGCCCTGGATCAACTGAAATAAACT
1 GAAGAAAGACCACCCTGG-TCAACTGAAATAAACT
* * *
24030 AAAGAAAGACCGCCCTGGGTCAACTAAAATAAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
* * *
24065 GAAGCAAGACCACCCTGGAACAACTGGAATAAACT
1 GAAGAAAGACCACCCTGG-TCAACTGAAATAAACT
** *
24100 GAAGAAAGGATAACCCTGGATCAACTGAAATTAACT
1 GAAGAAA-GACCACCCTGG-TCAACTGAAATAAACT
* * * *
24136 GAAGAAAGATCGCCCTGGATCAACTTGAAATTAGCT
1 GAAGAAAGACCACCCTGG-TCAAC-TGAAATAAACT
* *
24172 GAAGAAAGATCACCCTGGATCAACTTAAATAAACT
1 GAAGAAAGACCACCCTGG-TCAACTGAAATAAACT
*
24207 GAAGAAAGACCACCCTGGGTCAACTTAAATAAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
*
24242 GAAGAAAGACCACCCTGGGTCAACTAAAATAAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
** * * *
24277 GGGGAAAGATCGCCCTGGATCAATTGAAATTAAA-T
1 GAAGAAAGACCACCCTGG-TCAACTGAAA-TAAACT
24312 GAAGAAAGACCACCCTTGGTCAACTGAAA-ATAACT
1 GAAGAAAGACCACCC-TGGTCAACTGAAATA-AACT
* * * *
24347 GAAGAAAGATCGCCCTGGATCAACTGAACTTAACT
1 GAAGAAAGACCACCCTGG-TCAACTGAAATAAACT
* *
24382 GAAGAAAGATCGCCCTGGATCAACTGAAATAAACT
1 GAAGAAAGACCACCCTGG-TCAACTGAAATAAACT
*
24417 GAAGAAAGACCATCCTTGGTCAACTGAAAT-AACT
1 GAAGAAAGACCA-CCCTGGTCAACTGAAATAAACT
* *
24451 GAAGAAAGATCGCCCTGGATCAACTGAAACT-AACT
1 GAAGAAAGACCACCCTGG-TCAACTGAAA-TAAACT
* *
24486 GAGGAAAGATCACCCTGGATCAACTTGAAA-ACAACT
1 GAAGAAAGACCACCCTGG-TCAAC-TGAAATA-AACT
* * * *
24522 GAAAAAAGACCGCCCTAGGTCAACCGAAATTAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
* * * * * *
24557 AAAGGAAGATCGCCTTGGATCCA-TAGAAATAAACT
1 GAAGAAAGACCACCCTGG-TCAACT-GAAATAAACT
24592 GAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
* * *
24627 GAATAAAGACTGA-CCTGGGTCAGCTGAAATAAACT
1 GAAGAAAGAC-CACCCT-GGTCAACTGAAATAAACT
* * * * * *
24662 AAAGAAAGACCGCCCTGGGTCAACCGACATGAATT
1 GAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
24697 GAAGAAAGGACCACCCTAGGTCAACTGAAATAAACT
1 GAAGAAA-GACCACCCT-GGTCAACTGAAATAAACT
* *
24733 AAAGATAGAC
1 GAAGAAAGAC
24743 TTGAAATTAA
Statistics
Matches: 863, Mismatches: 129, Indels: 70
0.81 0.12 0.07
Matches are distributed among these distances:
33 24 0.03
34 67 0.08
35 612 0.71
36 158 0.18
37 2 0.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (34 bp):
GAAGAAAGACCACCCTGGTCAACTGAAATAAACT
Found at i:23872 original size:105 final size:105
Alignment explanation
Indices: 23652--24742 Score: 1098
Period size: 105 Copynumber: 10.4 Consensus size: 105
23642 GAATTGAAAG
* * * * *
23652 AAGACCTCCCTGGATCAA-TCG-AGTAAAATCGAAGAAAGACCACTCTGGGTCAAATGAAAT--A
1 AAGACCACCCTGGATCAACT-GAAATAAACT-GAAGAAAGACCACCCTGGGTCAACTGAAATAAA
* * * * *
23713 CTGAAGAACGACCACCCTCGATCATTCTGACATAAACTGAAGA
64 CTGAAGAAAGACCGCCCTGGATCA-ACTGAAATAAACTGAAGA
* * * *
23756 AAGACCACCCTAGG-TCAACTGAAATAAATTGAAAAAAGACCACCTTGGGTCAACTGAAATAAAT
1 AAGACCACCCT-GGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
23820 TGAAGAAAGACCACCCTGGGTCAATTGAAATAAACTGAAGA
65 TGAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGA
* * * * *
23861 AAGACCACCCTAGG-TCAACAGAAATAAACTGAAGAAAGACCGCCCTGGATTAA-TCGAAATAGA
1 AAGACCACCCT-GGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACT-GAAATAAA
* * * *
23924 CTGAAGAAAGACAG-CCTGGGTCAACTGAAATAAACTAAATA
64 CTGAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGA
* * * * * * * *
23965 AAGATCGCCCTGGATCAATTGAAATTAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACT
1 AAGACCACCCTGGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
* * * *
24030 AAAGAAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGC
66 GAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGA
* * ** * *
24070 AAGACCACCCTGGAACAACTGGAATAAACTGAAGAAAGGATAACCCTGGATCAACTGAAATTAAC
1 AAGACCACCCTGGATCAACTGAAATAAACTGAAGAAA-GACCACCCTGGGTCAACTGAAATAAAC
* * *
24135 TGAAGAAAGATCGCCCTGGATCAACTTGAAATTAGCTGAAGA
65 TGAAGAAAGACCGCCCTGGATCAAC-TGAAATAAACTGAAGA
* * *
24177 AAGATCACCCTGGATCAACTTAAATAAACTGAAGAAAGACCACCCTGGGTCAACTTAAATAAACT
1 AAGACCACCCTGGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
* * * **
24242 GAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGGGGA
66 GAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGA
* * * *
24282 AAGATCGCCCTGGATCAATTGAAATTAAA-TGAAGAAAGACCACCCTTGGTCAACTGAAA-ATAA
1 AAGACCACCCTGGATCAACTGAAA-TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATA-AA
* * *
24345 CTGAAGAAAGATCGCCCTGGATCAACTGAACTTAACTGAAGA
64 CTGAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGA
* * * *
24387 AAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCATCCTTGGTCAACTGAAAT-AACT
1 AAGACCACCCTGGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
* *
24451 GAAGAAAGATCGCCCTGGATCAACTGAAACT-AACTGAGGA
66 GAAGAAAGACCGCCCTGGATCAACTGAAA-TAAACTGAAGA
* * * * * *
24491 AAGATCACCCTGGATCAACTTGAAA-ACAACTGAAAAAAGACCGCCCTAGGTCAACCGAAATTAA
1 AAGACCACCCTGGATCAAC-TGAAATA-AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAA
* * * * *
24555 CTAAAGGAAGATCGCCTTGGATCCA-TAGAAATAAACTGAAGA
64 CTGAAGAAAGACCGCCCTGGATCAACT-GAAATAAACTGAAGA
* * * *
24597 AAGACCACCCTGGGTCAACTGAAATAAACTGAATAAAGACTGA-CCTGGGTCAGCTGAAATAAAC
1 AAGACCACCCTGGATCAACTGAAATAAACTGAAGAAAGAC-CACCCTGGGTCAACTGAAATAAAC
* * * * * *
24661 TAAAGAAAGACCGCCCTGGGTCAACCGACATGAATTGAAGA
65 TGAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGA
* *
24702 AAGGACCACCCTAGG-TCAACTGAAATAAACTAAAGATAGAC
1 AA-GACCACCCT-GGATCAACTGAAATAAACTGAAGAAAGAC
24743 TTGAAATTAA
Statistics
Matches: 835, Mismatches: 126, Indels: 50
0.83 0.12 0.05
Matches are distributed among these distances:
103 2 0.00
104 191 0.23
105 395 0.47
106 200 0.24
107 47 0.06
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (105 bp):
AAGACCACCCTGGATCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACT
GAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGA
Found at i:24747 original size:22 final size:22
Alignment explanation
Indices: 24722--24764 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24712 CTAGGTCAAC
24722 TGAAATAAACTAAAGATAGACT
1 TGAAATAAACTAAAGATAGACT
* *
24744 TGAAATTAACTGAAGATAGAC
1 TGAAATAAACTAAAGATAGAC
24765 CGCCCTAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (22 bp):
TGAAATAAACTAAAGATAGACT
Found at i:28374 original size:19 final size:18
Alignment explanation
Indices: 28341--28376 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28331 TTGAGATAAT
28341 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
28359 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
28377 TAAGTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:31397 original size:5 final size:5
Alignment explanation
Indices: 31382--31418 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
31372 GTAAAACATT
*
31382 AAAAC -AAAC AAAAC AAAAC AAACC AAAAC AAAAC AAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAA
31419 GCAACCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:31410 original size:15 final size:14
Alignment explanation
Indices: 31382--31418 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
31372 GTAAAACATT
31382 AAAACAAACAAAAC
1 AAAACAAACAAAAC
31396 AAAACAAACCAAAAC
1 AAAACAAA-CAAAAC
31411 AAAACAAA
1 AAAACAAA
31419 GCAACCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAACAAACAAAAC
Found at i:35865 original size:25 final size:25
Alignment explanation
Indices: 35829--35876 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
35819 ATGCAATATT
35829 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
35854 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
35877 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:36103 original size:28 final size:26
Alignment explanation
Indices: 36015--36113 Score: 99
Period size: 26 Copynumber: 3.7 Consensus size: 26
36005 AAGTGAACTC
* * * *
36015 AAAATGACCAACATGCCCCTGGATATG
1 AAAATGACCAAAATG-CCCTGAATGTA
* * *
36042 CAAATGACCAAAATGCCCTTAGTGTA
1 AAAATGACCAAAATGCCCTGAATGTA
*
36068 AAAATGACCATAATGCCACTGAATGTGA
1 AAAATGACCAAAATGCC-CTGAATGT-A
36096 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
36114 CTTAATTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
26 21 0.36
27 20 0.34
28 17 0.29
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.19
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCTGAATGTA
Found at i:40781 original size:90 final size:89
Alignment explanation
Indices: 40673--40841 Score: 275
Period size: 90 Copynumber: 1.9 Consensus size: 89
40663 CTAATTTATA
* * *
40673 ATAATTAATTAATTAGCTAACAAAGATTTAATTTGGAAGGAGTCCTGTTAACTAGAAGTCCAGAA
1 ATAATTAATTAATCAGCTAACAAAGATTTAATTTGGAAGGAGTCCTATTAACCAGAAGTCCAGAA
* *
40738 TCGTCAGAAGGAATGGTCCTAATTT
66 CCGACAG-AGGAATGGTCCTAATTT
*
40763 ATAATTAGTTAATCAGCTAACAAAGATTTAATTTGGAAGGAGTCCTATTAACCAGAAGTCCAGAA
1 ATAATTAATTAATCAGCTAACAAAGATTTAATTTGGAAGGAGTCCTATTAACCAGAAGTCCAGAA
40828 CCGACAGAGGAATG
66 CCGACAGAGGAATG
40842 ACCCTTGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 7 0.10
90 66 0.90
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (89 bp):
ATAATTAATTAATCAGCTAACAAAGATTTAATTTGGAAGGAGTCCTATTAACCAGAAGTCCAGAA
CCGACAGAGGAATGGTCCTAATTT
Found at i:41999 original size:33 final size:33
Alignment explanation
Indices: 41957--42093 Score: 274
Period size: 33 Copynumber: 4.2 Consensus size: 33
41947 ATTATTATTA
41957 TTATTGATCTTACATGATTTAATTTTTTAGTAG
1 TTATTGATCTTACATGATTTAATTTTTTAGTAG
41990 TTATTGATCTTACATGATTTAATTTTTTAGTAG
1 TTATTGATCTTACATGATTTAATTTTTTAGTAG
42023 TTATTGATCTTACATGATTTAATTTTTTAGTAG
1 TTATTGATCTTACATGATTTAATTTTTTAGTAG
42056 TTATTGATCTTACATGATTTAATTTTTTAGTAG
1 TTATTGATCTTACATGATTTAATTTTTTAGTAG
42089 TTATT
1 TTATT
42094 ATTTAATTCT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 104 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (33 bp):
TTATTGATCTTACATGATTTAATTTTTTAGTAG
Found at i:43927 original size:178 final size:177
Alignment explanation
Indices: 43474--43928 Score: 542
Period size: 179 Copynumber: 2.6 Consensus size: 177
43464 AAATTTTTCA
* *
43474 GAAGCTTTTTGATATTTGAAACATCAAATTTAGCTTTCGAGTTCTT-CATGAAAGTTGTAGATTA
1 GAAGCTTTTTGATATTTGAAACATTAAATTTAGCTTTCGAG-TCTTACATGAAAGTTGTAGATAA
* * * * * *
43538 CGCAACAACCTTTTAATAGACACTTGAATCATCTGAGTCGGACATCTGGAGCAAAAATTATGTAA
65 TGGAACAACCTTTTAATAGACACTTGAATCACCTAAGTCGGACATATGGAGCAAAAATTAAGTAA
* * * **
43603 TATTAAGTAGATCGTCCATTCCCGCTAACCGAAATAACTATTTTTTTG
130 TATTAAGTAGACCGTCAATTCCCGCTAACCGAAACAACTAACTTTTTG
* * *
43651 GAATCGTTTTTTTTATATTTGAAACATTAAA-TTAGCTTTCGAGTCCTTA-ATGAAAGTTATAGA
1 GAA--G-CTTTTTGATATTTGAAACATTAAATTTAGCTTTCGAGT-CTTACATGAAAGTTGTAGA
* * * *
43714 TAATGGAACAATCTTTTAAGAGACACTTAAATCACCTCAAG-CTGACATATGGAG-AAAAAGTTA
62 TAATGGAACAACCTTTTAATAGACACTTGAATCACCT-AAGTCGGACATATGGAGCAAAAA-TTA
* * *
43777 AGTAATATTAAGTGGACCGTCAATTTCCGTTAACCGAAACAACTAACTTTTTG
125 AGTAATATTAAGTAGACCGTCAATTCCCGCTAACCGAAACAACTAACTTTTTG
* * * *
43830 GAAGCATTTTTGATACTTGAGACATTAAATTTAGTTTTCGAGTCTTACATGAAAGTTGTAGATCA
1 GAAGC-TTTTTGATATTTGAAACATTAAATTTAGCTTTCGAGTCTTACATGAAAGTTGTAGATAA
* *
43895 TGGGACAACCTTTTAATAGACACTCGAATCACCT
65 TGGAACAACCTTTTAATAGACACTTGAATCACCT
43929 TGATCGAATA
Statistics
Matches: 233, Mismatches: 35, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
177 28 0.12
178 62 0.27
179 120 0.52
180 23 0.10
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (177 bp):
GAAGCTTTTTGATATTTGAAACATTAAATTTAGCTTTCGAGTCTTACATGAAAGTTGTAGATAAT
GGAACAACCTTTTAATAGACACTTGAATCACCTAAGTCGGACATATGGAGCAAAAATTAAGTAAT
ATTAAGTAGACCGTCAATTCCCGCTAACCGAAACAACTAACTTTTTG
Found at i:44912 original size:49 final size:47
Alignment explanation
Indices: 44821--44942 Score: 145
Period size: 49 Copynumber: 2.5 Consensus size: 47
44811 AATTTTGTAC
* * * * * **
44821 AAAAATTGATAAAAAGAGCAATGAAAAGTAAATATTCAATTTTATCTT
1 AAAAATTGAGAAAAAGTGC-AGGAAAAATAAAGATTCAATTTTATAGT
*
44869 AAAAATTGAGAAAAAGGTGCGAGGAAAAATAAAGATTCAATTTTGTAGT
1 AAAAATTGAGAAAAA-GTGC-AGGAAAAATAAAGATTCAATTTTATAGT
44918 AAAAATTGAGAAAAAGTGCAGGAAA
1 AAAAATTGAGAAAAAGTGCAGGAAA
44943 TGTAAAAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 6 0.09
48 18 0.28
49 40 0.62
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (47 bp):
AAAAATTGAGAAAAAGTGCAGGAAAAATAAAGATTCAATTTTATAGT
Found at i:53503 original size:19 final size:18
Alignment explanation
Indices: 53470--53505 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53460 TCGAGATAAT
53470 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
53488 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
53506 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:54762 original size:22 final size:22
Alignment explanation
Indices: 54734--54779 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
54724 AAAATTGGGG
54734 AAAATAAGATTAATCCAAAAAC
1 AAAATAAGATTAATCCAAAAAC
54756 AAAATAAGATTAATCCAAAAAC
1 AAAATAAGATTAATCCAAAAAC
54778 AA
1 AA
54780 TCAAATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.13, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAATAAGATTAATCCAAAAAC
Done.