Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009043.1 Corchorus capsularis cultivar CVL-1 contig09064, 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: 12555
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Found at i:2335 original size:27 final size:27
Alignment explanation
Indices: 2289--2364 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
2279 AAGTGAACTT
* *
2289 AAAATGACTCAAGATACCCCTAAATACA
1 AAAATGAC-CAAAATGCCCCTAAATACA
* * ***
2317 AAAATGGCCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTAAATACA
*
2344 GAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
2365 GGTGACCCTA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 31 0.82
28 7 0.18
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATACA
Found at i:2687 original size:63 final size:63
Alignment explanation
Indices: 2585--3114 Score: 468
Period size: 63 Copynumber: 8.5 Consensus size: 63
2575 AACTCTCGAG
* * * * *
2585 CAAGATTTTAG-ATTGAAA-TAGAAACTCTCGCCTATAGACCTCAATCAGGATTTAAAATGAA
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTTAAAATGAA
* * ** *
2646 CATGATTTTGGAATTGAAACAAGAAACTCTCGGCTAGAGACCTCAAGCAGGATTTAGAAAGGAA
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTTA-AAATGAA
* * ** *
2710 GC--TATGCTTGGAATTG----AAG--ACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAA
1 -CAAGAT-TTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTTAAAATG-A
2767 A
63 A
* * *
2768 CAAGA-CTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGAAATGAAA
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTTAAAATG-AA
* * * *
2831 CAAGA-TTTAG-ATTGAAACAAGAAACTCTTGACTAGAGACCTCGATTAGGATTTTGGAAACA-A
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGA-TTT--AAA-ATG
2893 AA
62 AA
* * **
2895 CAAGGTTTTGG-ATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTTGATGTGAAA
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTTAAAATG-AA
** * * *
2958 CAAGACATT-GAAATGAAACAAGAAACTCTTGACTAGAGACCTCAATTAGGATTTGGAAATGAAA
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTT-AAAATG-AA
* * * * *
3022 CTAGA-TTT-GAAATGAAACTAGAAACTCTCGATTAGAGACCTCGATTAGGATTTGAAAA-GAA
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTT-AAAATGAA
* *
3083 CAAGATTTAGGAAATGAAACAAGAAACTCTCG
1 CAAGATTTTGGAATTGAAACAAGAAACTCTCG
3115 CAGGATTTTA
Statistics
Matches: 398, Mismatches: 46, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
57 15 0.04
58 31 0.08
59 1 0.00
60 3 0.01
61 18 0.05
62 51 0.13
63 198 0.50
64 35 0.09
65 45 0.11
66 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (63 bp):
CAAGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAATTAGGATTTAAAATGAA
Found at i:2923 original size:127 final size:126
Alignment explanation
Indices: 2729--3112 Score: 506
Period size: 127 Copynumber: 3.0 Consensus size: 126
2719 GGAATTGAAG
* ** ** *
2729 ACTCTCGACTAGAGACCTCAAGCAGGATTT-GAAATGAAACAAGACTTGGAATTGAAACAAGAAA
1 ACTCTTGACTAGAGACCTCAATTAGGATTTGGAAACAAAACAAGATTTGG-ATTGAAACAAGAAA
*
2793 CTCTCGACTAGAGACCTCGATTAGGATTTGAAATGAAACAAGATTTAG-ATTGAAACAAGAA
65 CTCTCGACTAGAGACCTCGATTAGGATTTGAAATGAAACAAGATTTAGAAATGAAACAAGAA
* *
2854 ACTCTTGACTAGAGACCTCGATTAGGATTTTGGAAACAAAACAAGGTTTTGGATTGAAACAAGAA
1 ACTCTTGACTAGAGACCTCAATTAGGA-TTTGGAAACAAAACAA-GATTTGGATTGAAACAAGAA
* ** *
2919 ACTCTCGACTAGAGACCTCAATTAGGATTTGATGTGAAACAAGACATT-GAAATGAAACAAGAA
64 ACTCTCGACTAGAGACCTCGATTAGGATTTGAAATGAAACAAGA-TTTAGAAATGAAACAAGAA
** * * * *
2982 ACTCTTGACTAGAGACCTCAATTAGGATTTGGAAATGAAACTAGATTTGAAATGAAACTAGAAAC
1 ACTCTTGACTAGAGACCTCAATTAGGATTTGGAAACAAAACAAGATTTGGATTGAAACAAGAAAC
* *
3047 TCTCGATTAGAGACCTCGATTAGGATTTGAAAAG-AACAAGATTTAGGAAATGAAACAAGAA
66 TCTCGACTAGAGACCTCGATTAGGATTTGAAATGAAACAAGATTTA-GAAATGAAACAAGAA
3108 ACTCT
1 ACTCT
3113 CGCAGGATTT
Statistics
Matches: 225, Mismatches: 27, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
124 2 0.01
125 30 0.13
126 70 0.31
127 78 0.35
128 45 0.20
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (126 bp):
ACTCTTGACTAGAGACCTCAATTAGGATTTGGAAACAAAACAAGATTTGGATTGAAACAAGAAAC
TCTCGACTAGAGACCTCGATTAGGATTTGAAATGAAACAAGATTTAGAAATGAAACAAGAA
Found at i:2977 original size:190 final size:189
Alignment explanation
Indices: 2604--3114 Score: 555
Period size: 190 Copynumber: 2.7 Consensus size: 189
2594 AGATTGAAAT
* * * * * *
2604 AGAAACTCTCGCCTATAGACCTCAATCAGGATTT-AAAATG-AACATGATTTTGGAATTGAAACA
1 AGAAACTCTCGACTAGAGACCTCAATTAGGATTTGGAAATGAAACAAGA-TTT-GAAATGAAACA
* * ** * * * * *
2667 AGAAACTCTCGGCTAGAGACCTCAAGCAGGATTTAGAAAGGAAGCTATG-CTT-GGAATTG----
64 AGAAACTCTCGACTAGAGACCTCGATTAGGATTT-GAAA-AAAAC-AAGATTTAGGAAATGAAAC
*
2726 AAG--ACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACTTGGAATTGAAACA
126 AAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACTTGGAAATGAAACA
* *
2788 AGAAACTCTCGACTAGAGACCTCGATTAGGATTT-GAAATGAAACAAGATTT-AGATTGAAACAA
1 AGAAACTCTCGACTAGAGACCTCAATTAGGATTTGGAAATGAAACAAGATTTGA-AATGAAACAA
* * * *
2851 GAAACTCTTGACTAGAGACCTCGATTAGGATTTTGGAAACAAAACAAGGTTTTGG-ATTGAAACA
65 GAAACTCTCGACTAGAGACCTCGATTAGGA-TTT-GAAA-AAAACAAGATTTAGGAAATGAAACA
** **
2915 AGAAACTCTCGACTAGAGACCTCAATTAGGATTTGATGTGAAACAAGACATT-GAAATGAAACA
127 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGAC-TTGGAAATGAAACA
* * *
2978 AGAAACTCTTGACTAGAGACCTCAATTAGGATTTGGAAATGAAACTAGATTTGAAATGAAACTAG
1 AGAAACTCTCGACTAGAGACCTCAATTAGGATTTGGAAATGAAACAAGATTTGAAATGAAACAAG
* *
3043 AAACTCTCGATTAGAGACCTCGATTAGGATTTGAAAAGAACAAGATTTAGGAAATGAAACAAGAA
66 AAACTCTCGACTAGAGACCTCGATTAGGATTTGAAAAAAACAAGATTTAGGAAATGAAACAAGAA
3108 ACTCTCG
131 ACTCTCG
3115 CAGGATTTTA
Statistics
Matches: 279, Mismatches: 33, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
182 1 0.00
183 37 0.13
184 54 0.19
185 8 0.03
188 15 0.05
189 23 0.08
190 86 0.31
191 54 0.19
192 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (189 bp):
AGAAACTCTCGACTAGAGACCTCAATTAGGATTTGGAAATGAAACAAGATTTGAAATGAAACAAG
AAACTCTCGACTAGAGACCTCGATTAGGATTTGAAAAAAACAAGATTTAGGAAATGAAACAAGAA
ACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACTTGGAAATGAAACA
Found at i:3035 original size:17 final size:18
Alignment explanation
Indices: 3007--3043 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
2997 CCTCAATTAG
3007 GATTTGGAAATGAAACTA
1 GATTTGGAAATGAAACTA
3025 GATTT-GAAATGAAACTA
1 GATTTGGAAATGAAACTA
3042 GA
1 GA
3044 AACTCTCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (18 bp):
GATTTGGAAATGAAACTA
Found at i:3596 original size:114 final size:114
Alignment explanation
Indices: 3438--3646 Score: 282
Period size: 114 Copynumber: 1.8 Consensus size: 114
3428 AGGGAGAAAC
* * *
3438 TGATTAATCAATGATCCTAAATCAGGATTAAAATGTATTAATAAATCAATGATCCTAAACCAGGA
1 TGATAAATCAATGATCCTAAATCAGGATTAAAATGTATTAATAAAACAATGATCCCAAACCAGGA
*
3503 TTAAAATTAACTT-ATAAAGA-AATGATCCTAGATCAGGATTAACATGAAT
66 TTAAAA-TAAATTGATAAA-ATAATGATCCTAGATCAGGATTAACATGAAT
* * *
3552 TGATAAATCAATGATCCTAAATCAGGATTAACAT-TAACTT-ATAAAACAATGATCCCAGATCAG
1 TGATAAATCAATGATCCTAAATCAGGATTAAAATGT-A-TTAATAAAACAATGATCCCAAACCAG
*
3615 GATTAACATAAATTGATAAAATAATGATCCTA
64 GATTAAAATAAATTGATAAAATAATGATCCTA
3647 AATTAAAATT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
113 7 0.08
114 74 0.89
115 2 0.02
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.29
Consensus pattern (114 bp):
TGATAAATCAATGATCCTAAATCAGGATTAAAATGTATTAATAAAACAATGATCCCAAACCAGGA
TTAAAATAAATTGATAAAATAATGATCCTAGATCAGGATTAACATGAAT
Found at i:3659 original size:38 final size:38
Alignment explanation
Indices: 3447--3649 Score: 209
Period size: 38 Copynumber: 5.3 Consensus size: 38
3437 CTGATTAATC
* ** *
3447 AATGATCCTAAATCAGGATTAAAATGTATTAAT-AAAT
1 AATGATCCTAAATCAGGATTAACATAAATTGATAAAAT
* * *
3484 CAATGATCCTAAACCAGGATTAAAATTAACTT-ATAAAGA-
1 -AATGATCCTAAATCAGGATTAACA-TAAATTGATAAA-AT
* *
3523 AATGATCCTAGATCAGGATTAACATGAATTGAT-AAAT
1 AATGATCCTAAATCAGGATTAACATAAATTGATAAAAT
* *
3560 CAATGATCCTAAATCAGGATTAACATTAACTT-ATAAAAC
1 -AATGATCCTAAATCAGGATTAACA-TAAATTGATAAAAT
* *
3599 AATGATCCCAGATCAGGATTAACATAAATTGATAAAAT
1 AATGATCCTAAATCAGGATTAACATAAATTGATAAAAT
3637 AATGATCCTAAAT
1 AATGATCCTAAAT
3650 TAAAATTAAC
Statistics
Matches: 137, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
36 1 0.01
37 11 0.08
38 112 0.82
39 12 0.09
40 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (38 bp):
AATGATCCTAAATCAGGATTAACATAAATTGATAAAAT
Found at i:3659 original size:76 final size:77
Alignment explanation
Indices: 3446--3649 Score: 306
Period size: 76 Copynumber: 2.7 Consensus size: 77
3436 ACTGATTAAT
* * * * * *
3446 CAATGATCCTAAATCAGGATTAAAATGTATTAATAAATCAATGATCCTAAACCAGGATTAAAATT
1 CAATGATCCTAGATCAGGATTAACATGAATTGATAAATCAATGATCCTAAATCAGGATTAACATT
3511 AACTTATAAAGA
66 AACTTATAAAGA
3523 -AATGATCCTAGATCAGGATTAACATGAATTGATAAATCAATGATCCTAAATCAGGATTAACATT
1 CAATGATCCTAGATCAGGATTAACATGAATTGATAAATCAATGATCCTAAATCAGGATTAACATT
3587 AACTTATAAA-A
66 AACTTATAAAGA
* *
3598 CAATGATCCCAGATCAGGATTAACATAAATTGATAAAAT-AATGATCCTAAAT
1 CAATGATCCTAGATCAGGATTAACATGAATTGAT-AAATCAATGATCCTAAAT
3650 TAAAATTAAC
Statistics
Matches: 117, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
75 1 0.01
76 112 0.96
77 4 0.03
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (77 bp):
CAATGATCCTAGATCAGGATTAACATGAATTGATAAATCAATGATCCTAAATCAGGATTAACATT
AACTTATAAAGA
Found at i:3680 original size:76 final size:74
Alignment explanation
Indices: 3448--3680 Score: 181
Period size: 76 Copynumber: 3.1 Consensus size: 74
3438 TGATTAATCA
* * * ** *
3448 ATGATCCTAAATCAGGATTAAAATGTATTAATAAATCAATGATCCTAAACCAGGATTAAAATTAA
1 ATGATCCCAGATCAGGATTAACATAAATTGATAAATCAATGATCCT--A--A--ATTAAAATTAA
3513 CTTATAAAG---AA-
60 CTTATAAAGCATAAC
* * * ** *
3524 ATGATCCTAGATCAGGATTAACATGAATTGATAAATCAATGATCCTAAATCAGGATTAACAT-TA
1 ATGATCCCAGATCAGGATTAACATAAATTGATAAATCAATGATCCTAAATTAAAATTAACTTATA
***
3588 ACTTATAAAAC
66 AAGCAT--AAC
3599 AATGATCCCAGATCAGGATTAACATAAATTGATAAAAT-AATGATCCTAAATTAAAATTAACTTA
1 -ATGATCCCAGATCAGGATTAACATAAATTGAT-AAATCAATGATCCTAAATTAAAATTAACTTA
3663 TAAAGCAATAATC
64 TAAAGC-ATAA-C
3676 ATGAT
1 ATGAT
3681 TGAAATTAAA
Statistics
Matches: 127, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
69 3 0.02
70 10 0.08
72 1 0.01
74 3 0.02
76 100 0.79
77 8 0.06
78 2 0.02
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (74 bp):
ATGATCCCAGATCAGGATTAACATAAATTGATAAATCAATGATCCTAAATTAAAATTAACTTATA
AAGCATAAC
Found at i:4134 original size:36 final size:36
Alignment explanation
Indices: 4087--4270 Score: 152
Period size: 36 Copynumber: 5.2 Consensus size: 36
4077 ACCTGATAAA
4087 GACCACCCTGGATCAATTAAAATGCATGGAAGAACT
1 GACCACCCTGGATCAATTAAAATGCATGGAAGAACT
* * ** *
4123 GACCACCCTGGATCAAATAGACATAAATTGG-ATAA-T
1 GACCACCCTGGATCAATTA-AAATGCA-TGGAAGAACT
*** *
4159 GATTGCCCTGGATCAA--AATAA-AC-T-GAAGAA-T
1 GACCACCCTGGATCAATTAA-AATGCATGGAAGAACT
* * *
4190 GACCACCCTGGATCAACTAAAACGCATTGAA-AAGCT
1 GACCACCCTGGATCAATTAAAATGCATGGAAGAA-CT
*
4226 GACCACCCTGGATCAATTAAAATGCATGGACGAACT
1 GACCACCCTGGATCAATTAAAATGCATGGAAGAACT
4262 GACCACCCT
1 GACCACCCT
4271 TGAATCAACT
Statistics
Matches: 117, Mismatches: 19, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
30 1 0.01
31 18 0.15
32 2 0.02
33 5 0.04
34 5 0.04
35 3 0.03
36 71 0.61
37 9 0.08
38 3 0.03
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (36 bp):
GACCACCCTGGATCAATTAAAATGCATGGAAGAACT
Found at i:4366 original size:60 final size:60
Alignment explanation
Indices: 4277--4749 Score: 291
Period size: 70 Copynumber: 7.1 Consensus size: 60
4267 CCCTTGAATC
* * *
4277 AACTTGGAAACAACTGATGAAAAACCGCCCT-GAGTCGACTGAATCGATCATTCTGACATA
1 AACTTGGAAACTACTGAAGAAAGACCGCCCTAG-GTCGACTGAATCGATCATTCTGACATA
* * * *
4337 AACGTGGAAACTCCTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCTTTCTGTCACAAACTT
1 AACTTGGAAACTACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTG------AC--
4402 GGATA
58 --ATA
** *
4407 AACTTGGAAAAAACTGAAGAAAGACCTCCCTAGGTCGACTGAATCGATCATTCTGACATA
1 AACTTGGAAACTACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATA
* * *
4467 AACTTGGATAAACATGGCAACTACTGAAGAAAGACCACCCTAGGTCAACCGAATCGATCATTCTA
1 AACTTGG------A----AACTACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTC--
*
4532 ATACAAACTTGGATA
54 -T---GAC----ATA
* * *
4547 AACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATA
1 AACTTGGAAACTACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATA
*
4607 AACTTGGAATAAACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCT
1 AACTTGG---AAAC-T-------ACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCT
4672 GACATA
55 GACATA
* * *
4678 AACTTGGATACGTGGAAACTACTGAAGAAAGACCACCCTAGGTCGACCGAATCAATCATTCTGAC
1 AAC-----T---TGGAAACTACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGAC
*
4743 ACA
58 ATA
4746 AACT
1 AACT
4750 GAAGAAAGAC
Statistics
Matches: 331, Mismatches: 32, Indels: 97
0.72 0.07 0.21
Matches are distributed among these distances:
60 66 0.20
61 1 0.00
63 5 0.02
64 5 0.02
66 3 0.01
67 1 0.00
68 46 0.14
70 131 0.40
71 50 0.15
73 1 0.00
74 1 0.00
75 1 0.00
76 7 0.02
79 3 0.01
80 10 0.03
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (60 bp):
AACTTGGAAACTACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATA
Found at i:4642 original size:71 final size:70
Alignment explanation
Indices: 4334--4749 Score: 557
Period size: 70 Copynumber: 6.0 Consensus size: 70
4324 TCATTCTGAC
* ** * *
4334 ATAAACGTGGAAACTCCTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCTTTCTGTCACAAA
1 ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCATTCTGACACAAA
4399 CTTGG
66 CTTGG
* * * *
4404 ATAAACTTGGAAAAAACTGAAGAAAGACCTCCCTAGGTCGACTGAATCGATCATTCTGACATAAA
1 ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCATTCTGACACAAA
4469 CTTGG
66 CTTGG
* * * * * * *
4474 ATAAACATGGCAACTACTGAAGAAAGACCACCCTAGGTCAACCGAATCGATCATTCTAATACAAA
1 ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCATTCTGACACAAA
4539 CTTGG
66 CTTGG
* * * *
4544 ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAA
1 ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCATTCTGACACAAA
4609 CTTGG
66 CTTGG
* * * *
4614 AATAAACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAA
1 -ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCATTCTGACACAA
4679 ACTTGG
65 ACTTGG
* * * *
4685 AT--ACGTGGAAACTACTGAAGAAAGACCACCCTAGGTCGACCGAATCAATCATTCTGACACAAA
1 ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCATTCTGACACAAA
4748 CT
66 CT
4750 GAAGAAAGAC
Statistics
Matches: 307, Mismatches: 38, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
68 55 0.18
70 184 0.60
71 68 0.22
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (70 bp):
ATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACCGAATCGATCATTCTGACACAAA
CTTGG
Found at i:4784 original size:35 final size:35
Alignment explanation
Indices: 4745--4924 Score: 229
Period size: 35 Copynumber: 5.1 Consensus size: 35
4735 ATTCTGACAC
*
4745 AAACTGAAGAAAGACCGCCCTGGGTCAACCGAAAT
1 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAAT
* * *
4780 AAACTAAAGAAAAACCACCCTGGGTCAACTGAAAT
1 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAAT
* *
4815 AAACTGACGAAAGACCGCCCTGGGTCGACTG-AAT
1 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAAT
* * * * *
4849 CAAATTGAAGGAAGACCACCTTGAGTCAACTGAAAT
1 -AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAAT
4885 AAA-TCGAAGAAAGACCGCCCTGGGTCAACTGAAAT
1 AAACT-GAAGAAAGACCGCCCTGGGTCAACTGAAAT
4920 AAACT
1 AAACT
4925 TATACTTTTG
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
34 4 0.03
35 113 0.93
36 4 0.03
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (35 bp):
AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAAT
Found at i:5732 original size:16 final size:16
Alignment explanation
Indices: 5711--5743 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5701 AATTTGTTTT
5711 TTTTTTCTTTTTCTTA
1 TTTTTTCTTTTTCTTA
*
5727 TTTTTTCTTTTTTTTA
1 TTTTTTCTTTTTCTTA
5743 T
1 T
5744 CCAAAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTA
Found at i:6009 original size:19 final size:20
Alignment explanation
Indices: 5981--6018 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5971 AGCTCTATCT
5981 TTTTTCTCTTTCTTTTTTTC
1 TTTTTCTCTTTCTTTTTTTC
6001 TTTTT-TCTTTCTTTTTTT
1 TTTTTCTCTTTCTTTTTTT
6019 AGCTTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTCTCTTTCTTTTTTTC
Found at i:9782 original size:34 final size:36
Alignment explanation
Indices: 9739--9808 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
9729 CTTACCTTGA
9739 AAACCTTAGGATTGCC-A-TTTTTTTTTTGAAAACG
1 AAACCTTAGGATTGCCAATTTTTTTTTTTGAAAACG
9773 AAACCTTAGGATTGCCAATTTTTTTTTTTGAAAACG
1 AAACCTTAGGATTGCCAATTTTTTTTTTTGAAAACG
9809 GAATAAGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 16 0.47
35 1 0.03
36 17 0.50
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (36 bp):
AAACCTTAGGATTGCCAATTTTTTTTTTTGAAAACG
Done.